Starting phenix.real_space_refine on Sat Jul 20 12:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtr_36650/07_2024/8jtr_36650.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.023 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 105 5.49 5 S 21 5.16 5 C 6504 2.51 5 N 1997 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10957 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8708 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 45, 'TRANS': 1010} Chain breaks: 9 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 2249 Classifications: {'RNA': 105} Modifications used: {'rna2p_pur': 19, 'rna2p_pyr': 7, 'rna3p_pur': 39, 'rna3p_pyr': 40} Link IDs: {'rna2p': 26, 'rna3p': 78} Time building chain proxies: 7.03, per 1000 atoms: 0.64 Number of scatterers: 10957 At special positions: 0 Unit cell: (101.15, 103.7, 140.25, 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 21 16.00 P 105 15.00 O 2330 8.00 N 1997 7.00 C 6504 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 - 3.50 Amino acid : False - 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: 5.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 42.4% alpha, 8.7% beta 17 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 47 through 78 removed outlier: 3.588A pdb=" N ARG A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.576A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 4.136A pdb=" N VAL A 102 " --> pdb=" O TRP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.977A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.623A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.573A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.712A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.856A pdb=" N ARG A 384 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.661A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 470 through 491 Processing helix chain 'A' and resid 511 through 530 Processing helix chain 'A' and resid 531 through 531 No H-bonds generated for 'chain 'A' and resid 531 through 531' Processing helix chain 'A' and resid 533 through 536 Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.855A pdb=" N LYS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.664A pdb=" N LEU A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.636A pdb=" N LYS A 597 " --> pdb=" O TYR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.749A pdb=" N GLU A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.808A pdb=" N TYR A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.970A pdb=" N HIS A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.720A pdb=" N THR A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.558A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.976A pdb=" N GLN A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.560A pdb=" N SER A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 removed outlier: 3.532A pdb=" N SER A 797 " --> pdb=" O GLN A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 863 Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 944 through 951 removed outlier: 3.550A pdb=" N ILE A 948 " --> pdb=" O TYR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 removed outlier: 7.109A pdb=" N TYR A 3 " --> pdb=" O SER A 496 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N HIS A 498 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 5 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLU A 500 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 7 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 30 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 28 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 20 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 26 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 250 removed outlier: 5.326A pdb=" N ALA A 249 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 580 Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AA5, first strand: chain 'A' and resid 912 through 913 Processing sheet with id=AA6, first strand: chain 'A' and resid 937 through 938 removed outlier: 3.840A pdb=" N ARG A 928 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 943 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 937 through 938 removed outlier: 5.773A pdb=" N VAL A 929 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER A 979 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 7.632A pdb=" N SER A1033 " --> pdb=" O SER A1027 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER A1027 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG A1035 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A1025 " --> pdb=" O ARG A1035 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A1024 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A1009 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 988 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2528 1.33 - 1.45: 2866 1.45 - 1.57: 5752 1.57 - 1.69: 210 1.69 - 1.82: 36 Bond restraints: 11392 Sorted by residual: bond pdb=" CG PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 1.503 1.278 0.225 3.40e-02 8.65e+02 4.37e+01 bond pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.12e+01 bond pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.43e+00 bond pdb=" C ASP A 877 " pdb=" O ASP A 877 " ideal model delta sigma weight residual 1.235 1.225 0.009 4.70e-03 4.53e+04 4.08e+00 bond pdb=" CA PRO A 466 " pdb=" C PRO A 466 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.07e+00 ... (remaining 11387 not shown) Histogram of bond angle deviations from ideal: 89.07 - 98.15: 2 98.15 - 107.22: 903 107.22 - 116.29: 7431 116.29 - 125.36: 7012 125.36 - 134.44: 506 Bond angle restraints: 15854 Sorted by residual: angle pdb=" N PRO A 732 " pdb=" CD PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 103.20 89.07 14.13 1.50e+00 4.44e-01 8.87e+01 angle pdb=" CA PRO A 732 " pdb=" N PRO A 732 " pdb=" CD PRO A 732 " ideal model delta sigma weight residual 112.00 101.05 10.95 1.40e+00 5.10e-01 6.12e+01 angle pdb=" C GLN A 883 " pdb=" N GLU A 884 " pdb=" CA GLU A 884 " ideal model delta sigma weight residual 121.80 134.44 -12.64 2.44e+00 1.68e-01 2.68e+01 angle pdb=" CA PRO A 732 " pdb=" CB PRO A 732 " pdb=" CG PRO A 732 " ideal model delta sigma weight residual 104.50 96.19 8.31 1.90e+00 2.77e-01 1.91e+01 angle pdb=" N PRO A 732 " pdb=" CA PRO A 732 " pdb=" CB PRO A 732 " ideal model delta sigma weight residual 103.26 99.04 4.22 1.14e+00 7.69e-01 1.37e+01 ... (remaining 15849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 6688 34.82 - 69.65: 380 69.65 - 104.47: 49 104.47 - 139.30: 4 139.30 - 174.12: 5 Dihedral angle restraints: 7126 sinusoidal: 4020 harmonic: 3106 Sorted by residual: dihedral pdb=" O4' U B 29 " pdb=" C1' U B 29 " pdb=" N1 U B 29 " pdb=" C2 U B 29 " ideal model delta sinusoidal sigma weight residual -160.00 -45.00 -115.00 1 1.50e+01 4.44e-03 6.07e+01 dihedral pdb=" CA GLU A 243 " pdb=" C GLU A 243 " pdb=" N PRO A 244 " pdb=" CA PRO A 244 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O4' G B 99 " pdb=" C1' G B 99 " pdb=" N9 G B 99 " pdb=" C4 G B 99 " ideal model delta sinusoidal sigma weight residual 68.00 137.23 -69.23 1 1.70e+01 3.46e-03 2.14e+01 ... (remaining 7123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1551 0.052 - 0.103: 214 0.103 - 0.154: 34 0.154 - 0.206: 4 0.206 - 0.257: 1 Chirality restraints: 1804 Sorted by residual: chirality pdb=" CB ILE A 735 " pdb=" CA ILE A 735 " pdb=" CG1 ILE A 735 " pdb=" CG2 ILE A 735 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' A B 84 " pdb=" C4' A B 84 " pdb=" O3' A B 84 " pdb=" C2' A B 84 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1801 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 731 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 732 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 243 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 707 " -0.021 2.00e-02 2.50e+03 1.83e-02 8.33e+00 pdb=" CG TRP A 707 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 707 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 707 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 707 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 707 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 707 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 707 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 707 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 707 " 0.004 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1240 2.75 - 3.29: 10846 3.29 - 3.82: 17781 3.82 - 4.36: 21320 4.36 - 4.90: 34198 Nonbonded interactions: 85385 Sorted by model distance: nonbonded pdb=" O VAL A 227 " pdb=" O2' G B 16 " model vdw 2.212 2.440 nonbonded pdb=" NH1 ARG A 928 " pdb=" O VAL A1065 " model vdw 2.232 2.520 nonbonded pdb=" O2 C B 71 " pdb=" O2' A B 73 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASN A 653 " pdb=" N GLU A 654 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG A 821 " pdb=" OD2 ASP A 906 " model vdw 2.274 2.520 ... (remaining 85380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.170 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.003 0.225 11392 Z= 0.227 Angle : 0.631 14.125 15854 Z= 0.327 Chirality : 0.038 0.257 1804 Planarity : 0.006 0.115 1652 Dihedral : 20.053 174.122 5110 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.81 % Favored : 91.71 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 1037 helix: 0.99 (0.28), residues: 394 sheet: -0.83 (0.57), residues: 93 loop : -1.20 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 707 HIS 0.005 0.001 HIS A 702 PHE 0.016 0.001 PHE A 366 TYR 0.011 0.001 TYR A 864 ARG 0.009 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 665 ASP cc_start: 0.7436 (t0) cc_final: 0.7234 (t0) REVERT: A 854 MET cc_start: 0.6578 (tpt) cc_final: 0.6356 (tpt) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2573 time to fit residues: 46.0907 Evaluate side-chains 98 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN A 636 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11392 Z= 0.276 Angle : 0.671 10.250 15854 Z= 0.339 Chirality : 0.041 0.196 1804 Planarity : 0.005 0.079 1652 Dihedral : 21.880 177.985 2828 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.97 % Favored : 90.45 % Rotamer: Outliers : 2.01 % Allowed : 7.50 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 1037 helix: 1.09 (0.28), residues: 401 sheet: -1.08 (0.55), residues: 102 loop : -1.30 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 707 HIS 0.009 0.001 HIS A1028 PHE 0.015 0.002 PHE A1032 TYR 0.013 0.002 TYR A1013 ARG 0.004 0.001 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.014 Fit side-chains REVERT: A 153 ILE cc_start: 0.9030 (mm) cc_final: 0.8736 (mt) REVERT: A 964 TYR cc_start: 0.7562 (t80) cc_final: 0.7274 (t80) REVERT: A 971 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7926 (p) REVERT: A 972 GLU cc_start: 0.7779 (pp20) cc_final: 0.7462 (pp20) outliers start: 19 outliers final: 17 residues processed: 107 average time/residue: 0.2582 time to fit residues: 38.4750 Evaluate side-chains 112 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.0040 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11392 Z= 0.147 Angle : 0.573 9.037 15854 Z= 0.290 Chirality : 0.038 0.160 1804 Planarity : 0.004 0.064 1652 Dihedral : 21.737 171.026 2828 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.91 % Favored : 91.61 % Rotamer: Outliers : 1.37 % Allowed : 10.35 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 1037 helix: 1.33 (0.28), residues: 395 sheet: -1.28 (0.53), residues: 107 loop : -1.21 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 707 HIS 0.004 0.001 HIS A1072 PHE 0.013 0.001 PHE A 366 TYR 0.012 0.001 TYR A 562 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8999 (mm) cc_final: 0.8698 (mt) REVERT: A 474 MET cc_start: 0.7245 (tpp) cc_final: 0.6682 (tpp) REVERT: A 524 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8178 (ttmm) REVERT: A 623 ARG cc_start: 0.4230 (mmm160) cc_final: 0.3585 (tpm170) REVERT: A 665 ASP cc_start: 0.7492 (t0) cc_final: 0.7236 (t0) REVERT: A 972 GLU cc_start: 0.7777 (pp20) cc_final: 0.7405 (pp20) REVERT: A 1046 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6459 (mm-30) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.2512 time to fit residues: 37.5467 Evaluate side-chains 102 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11392 Z= 0.148 Angle : 0.558 7.913 15854 Z= 0.281 Chirality : 0.037 0.163 1804 Planarity : 0.004 0.049 1652 Dihedral : 21.654 170.795 2828 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.58 % Favored : 91.03 % Rotamer: Outliers : 2.11 % Allowed : 11.40 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 1037 helix: 1.35 (0.28), residues: 399 sheet: -1.36 (0.53), residues: 107 loop : -1.21 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 707 HIS 0.003 0.001 HIS A1028 PHE 0.016 0.001 PHE A 366 TYR 0.010 0.001 TYR A 668 ARG 0.003 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8996 (mm) cc_final: 0.8701 (mt) REVERT: A 383 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7713 (mp) REVERT: A 474 MET cc_start: 0.7187 (tpp) cc_final: 0.6882 (tpp) REVERT: A 524 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8190 (ttmm) REVERT: A 623 ARG cc_start: 0.4279 (mmm160) cc_final: 0.3765 (tpm170) REVERT: A 971 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7767 (p) REVERT: A 1046 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6475 (mm-30) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.2721 time to fit residues: 42.6300 Evaluate side-chains 109 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11392 Z= 0.201 Angle : 0.593 7.378 15854 Z= 0.300 Chirality : 0.038 0.169 1804 Planarity : 0.004 0.044 1652 Dihedral : 21.679 174.755 2828 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.78 % Favored : 90.84 % Rotamer: Outliers : 2.32 % Allowed : 13.09 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.27), residues: 1037 helix: 1.37 (0.28), residues: 398 sheet: -1.46 (0.53), residues: 107 loop : -1.26 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 PHE 0.013 0.002 PHE A 366 TYR 0.015 0.001 TYR A1013 ARG 0.004 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8988 (mm) cc_final: 0.8708 (mt) REVERT: A 474 MET cc_start: 0.7135 (tpp) cc_final: 0.6892 (tpp) REVERT: A 623 ARG cc_start: 0.4365 (mmm160) cc_final: 0.3948 (tpm170) REVERT: A 1046 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6511 (mm-30) outliers start: 22 outliers final: 18 residues processed: 113 average time/residue: 0.2648 time to fit residues: 41.9045 Evaluate side-chains 108 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 9 optimal weight: 0.0980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11392 Z= 0.188 Angle : 0.587 7.440 15854 Z= 0.296 Chirality : 0.038 0.162 1804 Planarity : 0.004 0.067 1652 Dihedral : 21.657 172.402 2828 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.06 % Favored : 90.65 % Rotamer: Outliers : 2.64 % Allowed : 14.36 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 1037 helix: 1.40 (0.28), residues: 397 sheet: -1.57 (0.53), residues: 107 loop : -1.25 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 PHE 0.013 0.001 PHE A 366 TYR 0.017 0.001 TYR A 864 ARG 0.003 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8988 (mm) cc_final: 0.8712 (mt) REVERT: A 383 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 474 MET cc_start: 0.7093 (tpp) cc_final: 0.6839 (tpp) REVERT: A 524 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8191 (ttmm) REVERT: A 623 ARG cc_start: 0.4351 (mmm160) cc_final: 0.3997 (tpm170) outliers start: 25 outliers final: 23 residues processed: 116 average time/residue: 0.2588 time to fit residues: 42.1559 Evaluate side-chains 116 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11392 Z= 0.158 Angle : 0.563 7.367 15854 Z= 0.284 Chirality : 0.037 0.164 1804 Planarity : 0.004 0.067 1652 Dihedral : 21.592 171.213 2828 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.39 % Favored : 91.32 % Rotamer: Outliers : 2.53 % Allowed : 15.73 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1037 helix: 1.43 (0.27), residues: 398 sheet: -1.37 (0.52), residues: 108 loop : -1.23 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 707 HIS 0.004 0.001 HIS A 340 PHE 0.013 0.001 PHE A 366 TYR 0.013 0.001 TYR A 668 ARG 0.002 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.8975 (mm) cc_final: 0.8696 (mt) REVERT: A 383 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 474 MET cc_start: 0.7062 (tpp) cc_final: 0.6804 (tpp) REVERT: A 623 ARG cc_start: 0.4392 (mmm160) cc_final: 0.4087 (tpm170) REVERT: A 665 ASP cc_start: 0.7392 (t70) cc_final: 0.7182 (t70) REVERT: A 977 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7459 (mmp80) REVERT: A 1046 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6488 (mm-30) outliers start: 24 outliers final: 21 residues processed: 109 average time/residue: 0.2685 time to fit residues: 41.3746 Evaluate side-chains 109 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11392 Z= 0.280 Angle : 0.656 9.268 15854 Z= 0.332 Chirality : 0.040 0.180 1804 Planarity : 0.005 0.065 1652 Dihedral : 21.733 175.651 2828 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.80 % Favored : 88.81 % Rotamer: Outliers : 3.06 % Allowed : 16.05 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 1037 helix: 1.28 (0.27), residues: 394 sheet: -1.63 (0.53), residues: 109 loop : -1.39 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 707 HIS 0.005 0.001 HIS A1028 PHE 0.016 0.002 PHE A1032 TYR 0.020 0.002 TYR A1013 ARG 0.005 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 153 ILE cc_start: 0.9006 (mm) cc_final: 0.8737 (mt) REVERT: A 383 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7744 (mp) REVERT: A 474 MET cc_start: 0.7185 (tpp) cc_final: 0.6934 (tpp) REVERT: A 623 ARG cc_start: 0.4604 (mmm160) cc_final: 0.4303 (tpm170) outliers start: 29 outliers final: 23 residues processed: 116 average time/residue: 0.2543 time to fit residues: 41.0869 Evaluate side-chains 116 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11392 Z= 0.258 Angle : 0.639 8.810 15854 Z= 0.323 Chirality : 0.040 0.174 1804 Planarity : 0.005 0.067 1652 Dihedral : 21.673 172.486 2828 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.45 % Favored : 90.16 % Rotamer: Outliers : 2.64 % Allowed : 16.90 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 1037 helix: 1.24 (0.28), residues: 394 sheet: -1.46 (0.56), residues: 99 loop : -1.48 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 707 HIS 0.007 0.001 HIS A1028 PHE 0.016 0.002 PHE A 852 TYR 0.018 0.001 TYR A 668 ARG 0.005 0.000 ARG A 862 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.057 Fit side-chains REVERT: A 153 ILE cc_start: 0.8998 (mm) cc_final: 0.8728 (mt) REVERT: A 383 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 474 MET cc_start: 0.7167 (tpp) cc_final: 0.6911 (tpp) REVERT: A 623 ARG cc_start: 0.4663 (mmm160) cc_final: 0.4382 (tpm170) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.2601 time to fit residues: 39.2358 Evaluate side-chains 110 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 0.0670 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11392 Z= 0.132 Angle : 0.568 8.337 15854 Z= 0.287 Chirality : 0.037 0.175 1804 Planarity : 0.004 0.069 1652 Dihedral : 21.485 168.648 2828 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.68 % Favored : 90.94 % Rotamer: Outliers : 1.90 % Allowed : 17.42 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.27), residues: 1037 helix: 1.33 (0.27), residues: 399 sheet: -1.35 (0.55), residues: 98 loop : -1.28 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 707 HIS 0.004 0.001 HIS A 146 PHE 0.020 0.001 PHE A 363 TYR 0.014 0.001 TYR A 922 ARG 0.006 0.000 ARG A 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.109 Fit side-chains REVERT: A 153 ILE cc_start: 0.8945 (mm) cc_final: 0.8656 (mt) REVERT: A 383 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 474 MET cc_start: 0.6949 (tpp) cc_final: 0.6650 (tpp) REVERT: A 568 GLU cc_start: 0.7059 (mp0) cc_final: 0.6544 (mp0) REVERT: A 623 ARG cc_start: 0.4538 (mmm160) cc_final: 0.4256 (tpm170) REVERT: A 977 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7315 (mmp80) REVERT: A 1060 ARG cc_start: 0.4802 (mtt180) cc_final: 0.4427 (mtt180) outliers start: 18 outliers final: 14 residues processed: 105 average time/residue: 0.2599 time to fit residues: 38.3399 Evaluate side-chains 106 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.0370 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 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 = 0.4380 r_free = 0.4380 target = 0.184750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139597 restraints weight = 17817.956| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.08 r_work: 0.3695 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11392 Z= 0.227 Angle : 0.609 11.056 15854 Z= 0.306 Chirality : 0.039 0.167 1804 Planarity : 0.004 0.067 1652 Dihedral : 21.515 172.562 2828 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.84 % Favored : 89.78 % Rotamer: Outliers : 2.11 % Allowed : 17.21 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 1037 helix: 1.38 (0.28), residues: 393 sheet: -1.31 (0.57), residues: 98 loop : -1.33 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 707 HIS 0.006 0.001 HIS A1028 PHE 0.019 0.002 PHE A 363 TYR 0.015 0.001 TYR A 668 ARG 0.019 0.001 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2247.75 seconds wall clock time: 40 minutes 56.80 seconds (2456.80 seconds total)