Starting phenix.real_space_refine on Thu Mar 14 15:54:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnv_34919/03_2024/8hnv_34919.pdb" } resolution = 3.1 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= 0.000 sd= 0.009 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 127 5.49 5 S 20 5.16 5 C 5381 2.51 5 N 1623 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A ASP 676": "OD1" <-> "OD2" Residue "A ASP 860": "OD1" <-> "OD2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5821 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 25, 'TRANS': 719} Chain breaks: 9 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2046 Classifications: {'RNA': 97} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 5, 'rna3p': 91} Chain breaks: 3 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 6.04, per 1000 atoms: 0.66 Number of scatterers: 9196 At special positions: 0 Unit cell: (119.6, 106.08, 108.16, 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 20 16.00 P 127 15.00 O 2045 8.00 N 1623 7.00 C 5381 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: 4.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 51.3% alpha, 10.6% beta 48 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 54 through 86 removed outlier: 4.032A pdb=" N SER A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.693A pdb=" N LEU A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.949A pdb=" N GLU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.944A pdb=" N HIS A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.572A pdb=" N LYS A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.986A pdb=" N LEU A 294 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.597A pdb=" N LYS A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.638A pdb=" N GLN A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 309 " --> pdb=" O TYR A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 309' Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.989A pdb=" N ASN A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.768A pdb=" N TRP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.985A pdb=" N LEU A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 417 through 430 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 467 through 489 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.947A pdb=" N THR A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 4.089A pdb=" N ASP A 719 " --> pdb=" O HIS A 715 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 829 through 832 removed outlier: 3.574A pdb=" N GLU A 832 " --> pdb=" O ARG A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 832' Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.136A pdb=" N TYR A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.989A pdb=" N TRP A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.667A pdb=" N ILE E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 30 - end of helix removed outlier: 3.523A pdb=" N SER E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 55 through 84 removed outlier: 4.188A pdb=" N ALA E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.744A pdb=" N ALA A 13 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.894A pdb=" N ASP A 37 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU A 25 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 35 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 496 removed outlier: 6.697A pdb=" N ILE A 494 " --> pdb=" O PHE A 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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 834 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 885 removed outlier: 4.392A pdb=" N PHE A 884 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 930 through 937 removed outlier: 3.750A pdb=" N PHE A 971 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 926 " --> pdb=" O PHE A 969 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 969 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1018 through 1022 removed outlier: 3.623A pdb=" N ILE A1004 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A1021 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1002 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 978 " --> pdb=" O TYR A1033 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1029 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A1034 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A1043 " --> pdb=" O GLN A1034 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 4.80 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: 2297 1.34 - 1.45: 2342 1.45 - 1.57: 4690 1.57 - 1.69: 249 1.69 - 1.81: 35 Bond restraints: 9613 Sorted by residual: bond pdb=" C3' U B 76 " pdb=" O3' U B 76 " ideal model delta sigma weight residual 1.427 1.449 -0.022 1.50e-02 4.44e+03 2.08e+00 bond pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" O3' U B 76 " pdb=" P U B 77 " ideal model delta sigma weight residual 1.607 1.625 -0.018 1.50e-02 4.44e+03 1.48e+00 bond pdb=" CA ASP A 959 " pdb=" CB ASP A 959 " ideal model delta sigma weight residual 1.531 1.563 -0.033 3.28e-02 9.30e+02 9.91e-01 bond pdb=" N TYR A 254 " pdb=" CA TYR A 254 " ideal model delta sigma weight residual 1.458 1.470 -0.012 1.42e-02 4.96e+03 6.86e-01 ... (remaining 9608 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.62: 873 106.62 - 113.48: 5414 113.48 - 120.34: 3531 120.34 - 127.21: 3439 127.21 - 134.07: 293 Bond angle restraints: 13550 Sorted by residual: angle pdb=" C3' U B 76 " pdb=" O3' U B 76 " pdb=" P U B 77 " ideal model delta sigma weight residual 120.20 126.20 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" CA TYR A 254 " pdb=" CB TYR A 254 " pdb=" CG TYR A 254 " ideal model delta sigma weight residual 113.90 120.96 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C GLU A 253 " pdb=" N TYR A 254 " pdb=" CA TYR A 254 " ideal model delta sigma weight residual 122.32 128.42 -6.10 1.76e+00 3.23e-01 1.20e+01 angle pdb=" C ASP A 109 " pdb=" N HIS A 110 " pdb=" CA HIS A 110 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" C CYS A 248 " pdb=" N THR A 249 " pdb=" CA THR A 249 " ideal model delta sigma weight residual 121.54 126.35 -4.81 1.91e+00 2.74e-01 6.35e+00 ... (remaining 13545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 5431 35.63 - 71.26: 389 71.26 - 106.88: 25 106.88 - 142.51: 2 142.51 - 178.14: 6 Dihedral angle restraints: 5853 sinusoidal: 3438 harmonic: 2415 Sorted by residual: dihedral pdb=" O4' U B 77 " pdb=" C1' U B 77 " pdb=" N1 U B 77 " pdb=" C2 U B 77 " ideal model delta sinusoidal sigma weight residual -160.00 18.14 -178.14 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 125 " pdb=" C1' U B 125 " pdb=" N1 U B 125 " pdb=" C2 U B 125 " ideal model delta sinusoidal sigma weight residual -128.00 30.10 -158.10 1 1.70e+01 3.46e-03 6.40e+01 dihedral pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " pdb=" P DA C 8 " ideal model delta sinusoidal sigma weight residual 220.00 46.94 173.06 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1236 0.036 - 0.072: 295 0.072 - 0.107: 68 0.107 - 0.143: 20 0.143 - 0.179: 5 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C3' G B 87 " pdb=" C4' G B 87 " pdb=" O3' G B 87 " pdb=" C2' G B 87 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" C3' G B 92 " pdb=" C4' G B 92 " pdb=" O3' G B 92 " pdb=" C2' G B 92 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" C3' C B 94 " pdb=" C4' C B 94 " pdb=" O3' C B 94 " pdb=" C2' C B 94 " both_signs ideal model delta sigma weight residual False -2.48 -2.32 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1621 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 253 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLU A 253 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A 253 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 254 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 166 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 167 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 974 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A 975 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.024 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 216 2.66 - 3.22: 8279 3.22 - 3.78: 15958 3.78 - 4.34: 21788 4.34 - 4.90: 32021 Nonbonded interactions: 78262 Sorted by model distance: nonbonded pdb=" O ILE A 891 " pdb=" O2' U B 56 " model vdw 2.103 2.440 nonbonded pdb=" O HIS A 98 " pdb=" O2' U B 59 " model vdw 2.134 2.440 nonbonded pdb=" O2' G B 69 " pdb=" O ASN E 26 " model vdw 2.158 2.440 nonbonded pdb=" OP1 U B 124 " pdb=" NZ LYS E 32 " model vdw 2.159 2.520 nonbonded pdb=" O2' G B 92 " pdb=" OP1 U B 93 " model vdw 2.162 2.440 ... (remaining 78257 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: 0.260 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: 1.850 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.830 Find NCS groups from input model: 0.220 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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 : 0.002 0.039 9613 Z= 0.146 Angle : 0.572 7.216 13550 Z= 0.303 Chirality : 0.035 0.179 1624 Planarity : 0.004 0.054 1264 Dihedral : 20.855 178.138 4277 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.30), residues: 810 helix: 0.77 (0.29), residues: 339 sheet: -0.99 (0.63), residues: 72 loop : -0.93 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 117 HIS 0.003 0.001 HIS A 191 PHE 0.017 0.001 PHE A 266 TYR 0.012 0.001 TYR A 164 ARG 0.005 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.827 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2423 time to fit residues: 35.3540 Evaluate side-chains 82 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 4.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1034 GLN E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9613 Z= 0.408 Angle : 0.748 8.802 13550 Z= 0.385 Chirality : 0.046 0.235 1624 Planarity : 0.006 0.060 1264 Dihedral : 22.105 177.471 2683 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.47 % Allowed : 11.62 % Favored : 86.91 % 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: -0.93 (0.29), residues: 810 helix: 0.19 (0.27), residues: 365 sheet: -0.69 (0.67), residues: 65 loop : -1.38 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 231 HIS 0.005 0.002 HIS A 123 PHE 0.018 0.002 PHE A 971 TYR 0.015 0.002 TYR A 254 ARG 0.005 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.819 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.1967 time to fit residues: 23.0199 Evaluate side-chains 74 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A1001 ASN E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9613 Z= 0.270 Angle : 0.622 6.476 13550 Z= 0.325 Chirality : 0.040 0.205 1624 Planarity : 0.005 0.060 1264 Dihedral : 22.003 177.662 2683 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.35 % Allowed : 14.41 % Favored : 83.24 % 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: -0.77 (0.29), residues: 810 helix: 0.42 (0.28), residues: 365 sheet: -0.77 (0.67), residues: 65 loop : -1.36 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 231 HIS 0.005 0.001 HIS A 679 PHE 0.013 0.002 PHE A 971 TYR 0.015 0.002 TYR A 254 ARG 0.004 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.902 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 80 average time/residue: 0.1959 time to fit residues: 22.8590 Evaluate side-chains 73 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9613 Z= 0.331 Angle : 0.682 9.710 13550 Z= 0.350 Chirality : 0.043 0.217 1624 Planarity : 0.005 0.060 1264 Dihedral : 22.079 175.442 2683 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.79 % Allowed : 16.76 % Favored : 80.44 % 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: -0.88 (0.29), residues: 810 helix: 0.30 (0.27), residues: 367 sheet: -1.00 (0.65), residues: 65 loop : -1.37 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 231 HIS 0.005 0.001 HIS A 679 PHE 0.020 0.002 PHE A 216 TYR 0.015 0.002 TYR A 254 ARG 0.004 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.764 Fit side-chains REVERT: A 35 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7547 (pp) outliers start: 19 outliers final: 11 residues processed: 82 average time/residue: 0.1895 time to fit residues: 22.8201 Evaluate side-chains 72 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9613 Z= 0.184 Angle : 0.562 6.959 13550 Z= 0.294 Chirality : 0.037 0.189 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.949 179.383 2683 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.38 % Allowed : 16.76 % Favored : 79.85 % 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: -0.51 (0.30), residues: 810 helix: 0.72 (0.28), residues: 371 sheet: -0.90 (0.65), residues: 65 loop : -1.31 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 231 HIS 0.002 0.001 HIS A 820 PHE 0.017 0.001 PHE A 216 TYR 0.013 0.001 TYR A 254 ARG 0.003 0.000 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.855 Fit side-chains REVERT: A 35 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 963 MET cc_start: 0.7244 (mmp) cc_final: 0.6835 (mmp) outliers start: 23 outliers final: 15 residues processed: 93 average time/residue: 0.1872 time to fit residues: 25.5954 Evaluate side-chains 82 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9613 Z= 0.169 Angle : 0.545 6.450 13550 Z= 0.284 Chirality : 0.037 0.188 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.865 179.596 2683 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.53 % Allowed : 17.65 % Favored : 78.82 % 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: -0.24 (0.30), residues: 810 helix: 0.97 (0.28), residues: 373 sheet: -0.68 (0.66), residues: 66 loop : -1.23 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 231 HIS 0.002 0.001 HIS A 820 PHE 0.017 0.001 PHE A 216 TYR 0.016 0.001 TYR A 254 ARG 0.003 0.000 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 1.366 Fit side-chains REVERT: A 35 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7350 (pp) outliers start: 24 outliers final: 16 residues processed: 98 average time/residue: 0.1943 time to fit residues: 28.1289 Evaluate side-chains 88 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9613 Z= 0.209 Angle : 0.571 7.486 13550 Z= 0.296 Chirality : 0.038 0.212 1624 Planarity : 0.004 0.059 1264 Dihedral : 21.863 178.887 2683 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.94 % Allowed : 18.97 % Favored : 78.09 % 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: -0.27 (0.30), residues: 810 helix: 1.01 (0.28), residues: 365 sheet: -0.83 (0.66), residues: 65 loop : -1.25 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 231 HIS 0.003 0.001 HIS A 495 PHE 0.018 0.002 PHE A 216 TYR 0.015 0.001 TYR A 254 ARG 0.002 0.000 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.644 Fit side-chains REVERT: A 35 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7375 (pp) REVERT: A 780 SER cc_start: 0.3842 (t) cc_final: 0.3586 (p) outliers start: 20 outliers final: 16 residues processed: 91 average time/residue: 0.1900 time to fit residues: 25.0790 Evaluate side-chains 88 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9613 Z= 0.151 Angle : 0.537 7.483 13550 Z= 0.282 Chirality : 0.036 0.183 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.830 179.331 2683 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 19.56 % Favored : 77.94 % 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: -0.10 (0.30), residues: 810 helix: 1.17 (0.28), residues: 365 sheet: -0.61 (0.67), residues: 66 loop : -1.21 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 PHE 0.019 0.001 PHE A 216 TYR 0.017 0.001 TYR A 254 ARG 0.003 0.000 ARG A1043 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.825 Fit side-chains REVERT: A 35 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7343 (pp) REVERT: A 780 SER cc_start: 0.3770 (t) cc_final: 0.3530 (p) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 0.1954 time to fit residues: 25.2760 Evaluate side-chains 85 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9613 Z= 0.315 Angle : 0.652 6.903 13550 Z= 0.337 Chirality : 0.042 0.215 1624 Planarity : 0.005 0.060 1264 Dihedral : 21.976 176.635 2683 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.50 % Allowed : 20.74 % Favored : 76.76 % 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: -0.50 (0.29), residues: 810 helix: 0.76 (0.28), residues: 361 sheet: -0.83 (0.67), residues: 60 loop : -1.30 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 231 HIS 0.005 0.001 HIS A 679 PHE 0.024 0.002 PHE A 216 TYR 0.014 0.002 TYR A 254 ARG 0.005 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.843 Fit side-chains REVERT: A 35 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 678 MET cc_start: 0.6385 (ttt) cc_final: 0.6130 (ttt) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.1898 time to fit residues: 23.6195 Evaluate side-chains 84 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 ASN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9613 Z= 0.155 Angle : 0.536 5.957 13550 Z= 0.281 Chirality : 0.036 0.183 1624 Planarity : 0.004 0.059 1264 Dihedral : 21.816 179.594 2683 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 20.74 % Favored : 76.76 % 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: -0.15 (0.30), residues: 810 helix: 1.05 (0.28), residues: 372 sheet: -0.62 (0.67), residues: 66 loop : -1.19 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 231 HIS 0.002 0.001 HIS A 820 PHE 0.018 0.001 PHE A 216 TYR 0.016 0.001 TYR A 254 ARG 0.003 0.000 ARG A1043 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.873 Fit side-chains REVERT: A 35 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7344 (pp) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.1700 time to fit residues: 21.9559 Evaluate side-chains 82 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.193781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173247 restraints weight = 11014.197| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 0.85 r_work: 0.3766 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 9613 Z= 0.207 Angle : 0.840 59.199 13550 Z= 0.497 Chirality : 0.039 0.572 1624 Planarity : 0.004 0.071 1264 Dihedral : 21.814 179.632 2683 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.06 % Allowed : 21.18 % Favored : 76.76 % Cbeta Deviations : 0.13 % 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: -0.14 (0.30), residues: 810 helix: 1.06 (0.28), residues: 372 sheet: -0.61 (0.67), residues: 66 loop : -1.19 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 231 HIS 0.002 0.001 HIS A 679 PHE 0.014 0.001 PHE A 216 TYR 0.016 0.001 TYR A 254 ARG 0.002 0.000 ARG A1043 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.93 seconds wall clock time: 30 minutes 3.37 seconds (1803.37 seconds total)