Starting phenix.real_space_refine on Tue Aug 4 23:43:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yxm_73611/08_2026/9yxm_73611_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yxm_73611/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9yxm_73611/08_2026/9yxm_73611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yxm_73611/08_2026/9yxm_73611.map" model { file = "/net/cci-nas-00/data/ceres_data/9yxm_73611/08_2026/9yxm_73611_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yxm_73611/08_2026/9yxm_73611_neut.cif" } 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-2.2rc3-6140/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: 1.51, per 1000 atoms: 0.21 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: 0.65 Conformation dependent library (CDL) restraints added in 359.6 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: 0.94 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: 0.98 Time building geometry restraints manager: 0.85 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: 10152 2.67 - 5.34: 351 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: 1097 0.128 - 0.256: 64 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- 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= 0.429 Angle : 1.206 13.340 10573 Z= 0.734 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 1.20592 / 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 : 0.247 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: 0.0942 time to fit residues: 13.1174 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 : 0.238 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.066170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048072 restraints weight = 70311.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.050000 restraints weight = 47491.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051232 restraints weight = 36368.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.052080 restraints weight = 30695.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.052410 restraints weight = 27251.097| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 7618 Z= 0.247 Angle : 0.920 11.065 10573 Z= 0.500 Chirality : 0.054 0.302 1168 Planarity : 0.006 0.042 1136 Dihedral : 27.035 179.741 1528 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.00 % Favored : 89.61 % Rotamer: Outliers : 0.32 % Allowed : 5.72 % 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: -1.60 (0.29), residues: 760 helix: -0.47 (0.24), residues: 414 sheet: -3.95 (0.87), residues: 20 loop : -1.56 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 792 TYR 0.019 0.002 TYR A 44 PHE 0.040 0.003 PHE A 400 TRP 0.019 0.002 TRP A 727 HIS 0.006 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.25 ( 7618) covalent geometry : angle 0.91959 / 0.50 (10573) hydrogen bonds : bond 0.08614 / 5.77 ( 334) hydrogen bonds : angle 5.78762 / 4.19 ( 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 85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.234 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: 0.7438 (mtp) cc_final: 0.4644 (mmm) REVERT: A 141 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 155 ARG cc_start: 0.9647 (ppt170) cc_final: 0.9365 (ptt-90) REVERT: A 847 ASP cc_start: 0.9540 (m-30) cc_final: 0.9193 (p0) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.1012 time to fit residues: 11.2951 Evaluate side-chains 65 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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: 9.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.082915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071670 restraints weight = 87812.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.073365 restraints weight = 51909.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.074490 restraints weight = 35380.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.075232 restraints weight = 26766.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.075626 restraints weight = 21987.425| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7618 Z= 0.227 Angle : 0.867 8.582 10573 Z= 0.476 Chirality : 0.053 0.335 1168 Planarity : 0.006 0.095 1136 Dihedral : 27.102 177.279 1528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 32.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.16 % Favored : 91.45 % Rotamer: Outliers : 0.16 % Allowed : 6.68 % Favored : 93.16 % 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: -1.79 (0.29), residues: 760 helix: -0.54 (0.24), residues: 409 sheet: -3.84 (0.89), residues: 24 loop : -1.73 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.016 0.002 TYR A 739 PHE 0.054 0.003 PHE A 400 TRP 0.013 0.002 TRP A 201 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 ( 7618) covalent geometry : angle 0.86701 / 0.48 (10573) hydrogen bonds : bond 0.07315 / 4.88 ( 334) hydrogen bonds : angle 5.73853 / 4.11 ( 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 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.157 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 141 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 193 LYS cc_start: 0.9519 (pptt) cc_final: 0.9114 (tptp) REVERT: A 847 ASP cc_start: 0.9516 (m-30) cc_final: 0.9154 (p0) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0844 time to fit residues: 9.6267 Evaluate side-chains 56 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.0010 overall best weight: 2.5792 ------------------------------------------------------------------------------- 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** A 784 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.083284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.071830 restraints weight = 88845.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.073573 restraints weight = 52251.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.074658 restraints weight = 35670.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.075396 restraints weight = 27275.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.075831 restraints weight = 22445.199| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7618 Z= 0.187 Angle : 0.841 11.949 10573 Z= 0.452 Chirality : 0.051 0.338 1168 Planarity : 0.006 0.064 1136 Dihedral : 27.118 176.621 1528 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.13 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: -1.82 (0.29), residues: 760 helix: -0.61 (0.24), residues: 409 sheet: -3.52 (0.90), residues: 24 loop : -1.70 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.017 0.002 TYR A 518 PHE 0.037 0.002 PHE A 400 TRP 0.037 0.002 TRP A 620 HIS 0.017 0.001 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 ( 7618) covalent geometry : angle 0.84085 / 0.45 (10573) hydrogen bonds : bond 0.06322 / 4.30 ( 334) hydrogen bonds : angle 5.69537 / 4.08 ( 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 79 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.254 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: A 93 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8263 (ptpp) REVERT: A 193 LYS cc_start: 0.9493 (pptt) cc_final: 0.9088 (tptp) REVERT: A 549 MET cc_start: 0.7105 (tpt) cc_final: 0.6853 (tpt) REVERT: A 835 THR cc_start: 0.8893 (p) cc_final: 0.8687 (p) REVERT: A 847 ASP cc_start: 0.9502 (m-30) cc_final: 0.9152 (p0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0896 time to fit residues: 9.6727 Evaluate side-chains 60 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.057294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.041461 restraints weight = 71648.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.043085 restraints weight = 48848.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.044084 restraints weight = 38208.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.044392 restraints weight = 32645.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044927 restraints weight = 30827.885| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7618 Z= 0.242 Angle : 0.861 9.698 10573 Z= 0.472 Chirality : 0.053 0.342 1168 Planarity : 0.005 0.057 1136 Dihedral : 27.067 177.173 1528 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 40.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.00 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.29), residues: 760 helix: -0.69 (0.23), residues: 408 sheet: -3.69 (0.67), residues: 38 loop : -1.71 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 720 TYR 0.014 0.002 TYR A 308 PHE 0.029 0.003 PHE A 400 TRP 0.016 0.002 TRP A 328 HIS 0.007 0.002 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 ( 7618) covalent geometry : angle 0.86140 / 0.47 (10573) hydrogen bonds : bond 0.08616 / 5.79 ( 334) hydrogen bonds : angle 5.72409 / 4.08 ( 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 : 0.271 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: 0.7818 (tpt) cc_final: 0.7293 (tpt) REVERT: A 193 LYS cc_start: 0.9486 (pptt) cc_final: 0.9069 (tptp) REVERT: A 793 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8898 (ptpt) REVERT: A 847 ASP cc_start: 0.9540 (m-30) cc_final: 0.9187 (p0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0929 time to fit residues: 9.7574 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 : 0.256 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.059938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.043832 restraints weight = 71327.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045730 restraints weight = 46718.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046895 restraints weight = 35456.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047543 restraints weight = 29745.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048102 restraints weight = 26800.472| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7618 Z= 0.194 Angle : 0.850 10.774 10573 Z= 0.459 Chirality : 0.052 0.362 1168 Planarity : 0.005 0.041 1136 Dihedral : 27.087 175.438 1528 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 34.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.61 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -1.92 (0.29), residues: 760 helix: -0.64 (0.24), residues: 410 sheet: -3.67 (0.69), residues: 38 loop : -1.70 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 84 TYR 0.016 0.002 TYR A 739 PHE 0.031 0.002 PHE A 849 TRP 0.012 0.001 TRP A 201 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7618) covalent geometry : angle 0.84987 / 0.46 (10573) hydrogen bonds : bond 0.06251 / 4.29 ( 334) hydrogen bonds : angle 5.67991 / 4.07 ( 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 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.260 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 193 LYS cc_start: 0.9494 (pptt) cc_final: 0.9082 (tptp) REVERT: A 800 GLU cc_start: 0.9066 (tp30) cc_final: 0.8816 (mm-30) REVERT: A 847 ASP cc_start: 0.9526 (m-30) cc_final: 0.9190 (p0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0884 time to fit residues: 9.2695 Evaluate side-chains 58 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 chunk 36 optimal weight: 8.9990 overall best weight: 1.8824 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.060594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.044521 restraints weight = 71324.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.046425 restraints weight = 46271.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.047573 restraints weight = 34862.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048341 restraints weight = 29223.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.048787 restraints weight = 25984.551| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7618 Z= 0.177 Angle : 0.834 10.717 10573 Z= 0.449 Chirality : 0.051 0.347 1168 Planarity : 0.005 0.042 1136 Dihedral : 27.100 175.469 1528 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.26 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.85 (0.29), residues: 760 helix: -0.56 (0.24), residues: 410 sheet: -3.56 (0.89), residues: 24 loop : -1.84 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 155 TYR 0.014 0.001 TYR A 739 PHE 0.028 0.002 PHE A 849 TRP 0.010 0.001 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 0.83353 / 0.45 (10573) hydrogen bonds : bond 0.05653 / 3.86 ( 334) hydrogen bonds : angle 5.54998 / 3.97 ( 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 75 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.244 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 93 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8230 (ptpp) REVERT: A 193 LYS cc_start: 0.9495 (pptt) cc_final: 0.9091 (tptp) REVERT: A 800 GLU cc_start: 0.9076 (tp30) cc_final: 0.8834 (mm-30) REVERT: A 847 ASP cc_start: 0.9520 (m-30) cc_final: 0.9208 (p0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0880 time to fit residues: 9.1885 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 : 0.270 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- 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 737 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 = 0.3711 r_free = 0.3711 target = 0.081122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.069984 restraints weight = 88732.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.071668 restraints weight = 51865.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.072782 restraints weight = 35656.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073503 restraints weight = 26931.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.073789 restraints weight = 22119.027| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7618 Z= 0.179 Angle : 0.827 11.172 10573 Z= 0.445 Chirality : 0.050 0.343 1168 Planarity : 0.005 0.040 1136 Dihedral : 27.067 175.923 1528 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.47 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 760 helix: -0.49 (0.24), residues: 404 sheet: -3.58 (0.87), residues: 24 loop : -1.84 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 478 TYR 0.012 0.001 TYR A 739 PHE 0.028 0.002 PHE A 849 TRP 0.011 0.001 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 ( 7618) covalent geometry : angle 0.82687 / 0.44 (10573) hydrogen bonds : bond 0.05749 / 3.91 ( 334) hydrogen bonds : angle 5.58874 / 3.98 ( 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 : 0.208 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 44 TYR cc_start: 0.8824 (m-80) cc_final: 0.7194 (t80) REVERT: A 46 MET cc_start: 0.8053 (tpt) cc_final: 0.7622 (tpt) REVERT: A 93 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8283 (ptpp) REVERT: A 193 LYS cc_start: 0.9543 (pptt) cc_final: 0.9138 (tptp) REVERT: A 677 MET cc_start: 0.9501 (mmp) cc_final: 0.9287 (mmm) REVERT: A 800 GLU cc_start: 0.9066 (tp30) cc_final: 0.8850 (mm-30) REVERT: A 847 ASP cc_start: 0.9504 (m-30) cc_final: 0.9192 (p0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0894 time to fit residues: 9.3164 Evaluate side-chains 53 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 41 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 overall best weight: 2.1762 ------------------------------------------------------------------------------- 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 737 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 = 0.080777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.069757 restraints weight = 87360.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.071435 restraints weight = 51555.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.072536 restraints weight = 35334.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.073189 restraints weight = 26721.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073693 restraints weight = 22272.639| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7618 Z= 0.178 Angle : 0.842 14.545 10573 Z= 0.452 Chirality : 0.051 0.344 1168 Planarity : 0.005 0.042 1136 Dihedral : 27.049 175.979 1528 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 31.43 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.13 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.74 (0.29), residues: 760 helix: -0.47 (0.24), residues: 409 sheet: -3.10 (0.92), residues: 22 loop : -1.83 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.012 0.002 TYR A 739 PHE 0.027 0.002 PHE A 849 TRP 0.013 0.001 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 7618) covalent geometry : angle 0.84179 / 0.45 (10573) hydrogen bonds : bond 0.05631 / 3.83 ( 334) hydrogen bonds : angle 5.61814 / 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 : 0.276 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: A 44 TYR cc_start: 0.8832 (m-80) cc_final: 0.7100 (t80) REVERT: A 46 MET cc_start: 0.7412 (tpt) cc_final: 0.7002 (tpt) REVERT: A 93 LYS cc_start: 0.8189 (ptpp) cc_final: 0.7908 (ptpp) REVERT: A 193 LYS cc_start: 0.9558 (pptt) cc_final: 0.9131 (tptp) REVERT: A 677 MET cc_start: 0.9497 (mmp) cc_final: 0.9265 (mmm) REVERT: A 847 ASP cc_start: 0.9445 (m-30) cc_final: 0.9059 (p0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0893 time to fit residues: 9.2903 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 : 0.243 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3584 r_free = 0.3584 target = 0.062909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.046923 restraints weight = 67144.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.049067 restraints weight = 41208.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050440 restraints weight = 29677.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.051316 restraints weight = 23963.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051874 restraints weight = 20834.108| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7618 Z= 0.166 Angle : 0.840 10.624 10573 Z= 0.450 Chirality : 0.051 0.341 1168 Planarity : 0.005 0.044 1136 Dihedral : 27.044 175.704 1528 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.08 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -1.78 (0.30), residues: 760 helix: -0.53 (0.24), residues: 410 sheet: -3.04 (0.93), residues: 24 loop : -1.81 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 155 TYR 0.012 0.002 TYR A 312 PHE 0.028 0.002 PHE A 849 TRP 0.015 0.002 TRP A 502 HIS 0.007 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 ( 7618) covalent geometry : angle 0.84012 / 0.45 (10573) hydrogen bonds : bond 0.04903 / 3.33 ( 334) hydrogen bonds : angle 5.60790 / 3.98 ( 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 73 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.255 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 44 TYR cc_start: 0.8760 (m-80) cc_final: 0.7204 (t80) REVERT: A 46 MET cc_start: 0.8332 (tpt) cc_final: 0.7878 (tpt) REVERT: A 93 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8172 (ptpp) REVERT: A 190 MET cc_start: 0.9415 (ptp) cc_final: 0.9091 (pmm) REVERT: A 193 LYS cc_start: 0.9500 (pptt) cc_final: 0.9110 (tptp) REVERT: A 677 MET cc_start: 0.9407 (mmp) cc_final: 0.9203 (mmm) REVERT: A 847 ASP cc_start: 0.9513 (m-30) cc_final: 0.9241 (p0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0954 time to fit residues: 9.5335 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 : 0.255 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 14 optimal weight: 0.0270 chunk 79 optimal weight: 9.9990 overall best weight: 3.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 726 HIS ** 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 = 0.3491 r_free = 0.3491 target = 0.059276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.043766 restraints weight = 70644.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.045701 restraints weight = 44362.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047052 restraints weight = 32477.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.047808 restraints weight = 26167.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.048096 restraints weight = 23268.820| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7618 Z= 0.218 Angle : 0.860 10.065 10573 Z= 0.464 Chirality : 0.052 0.335 1168 Planarity : 0.005 0.045 1136 Dihedral : 27.000 177.400 1528 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 38.48 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.74 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.72 (0.30), residues: 760 helix: -0.49 (0.24), residues: 404 sheet: -3.23 (0.86), residues: 24 loop : -1.74 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG A 756 TYR 0.012 0.002 TYR A 116 PHE 0.028 0.002 PHE A 849 TRP 0.014 0.002 TRP A 727 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 ( 7618) covalent geometry : angle 0.85964 / 0.46 (10573) hydrogen bonds : bond 0.07726 / 5.17 ( 334) hydrogen bonds : angle 5.79068 / 4.14 ( 935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.41 seconds wall clock time: 26 minutes 25.51 seconds (1585.51 seconds total)