Starting phenix.real_space_refine on Sat Jul 20 23:42:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2k_27141/07_2024/8d2k_27141_neut.cif" } resolution = 2.43 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 156 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6940 2.51 5 N 2220 2.21 5 O 2949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ASP 812": "OD1" <-> "OD2" 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: 12295 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNA': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 47, 'rna3p_pyr': 41} Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 12} Chain: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.87, per 1000 atoms: 0.64 Number of scatterers: 12295 At special positions: 0 Unit cell: (94.05, 106.425, 129.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 156 15.00 Mg 10 11.99 O 2949 8.00 N 2220 7.00 C 6940 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 50.6% alpha, 9.8% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 406 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 441 through 456 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 553 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.653A pdb=" N ARG A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.809A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 746 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 4.140A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1071 removed outlier: 3.687A pdb=" N ALA A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.914A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 824 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 956 removed outlier: 3.587A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.390A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 7.04 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: 2214 1.33 - 1.45: 3804 1.45 - 1.57: 6203 1.57 - 1.69: 306 1.69 - 1.81: 28 Bond restraints: 12555 Sorted by residual: bond pdb=" C3' G B 97 " pdb=" O3' G B 97 " ideal model delta sigma weight residual 1.427 1.480 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " ideal model delta sigma weight residual 1.422 1.517 -0.095 3.00e-02 1.11e+03 1.01e+01 bond pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.50e-02 4.44e+03 8.35e+00 bond pdb=" C3' DA X 1 " pdb=" O3' DA X 1 " ideal model delta sigma weight residual 1.422 1.502 -0.080 3.00e-02 1.11e+03 7.18e+00 bond pdb=" CB TRP A1128 " pdb=" CG TRP A1128 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.16e+00 ... (remaining 12550 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.10: 1088 106.10 - 113.16: 6822 113.16 - 120.22: 4773 120.22 - 127.28: 4623 127.28 - 134.34: 441 Bond angle restraints: 17747 Sorted by residual: angle pdb=" C3' G B 97 " pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 120.20 132.67 -12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " pdb=" P DT D 30 " ideal model delta sigma weight residual 120.20 127.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" N GLU A 548 " pdb=" CA GLU A 548 " pdb=" CB GLU A 548 " ideal model delta sigma weight residual 110.28 118.15 -7.87 1.55e+00 4.16e-01 2.58e+01 angle pdb=" C3' C B 96 " pdb=" O3' C B 96 " pdb=" P G B 97 " ideal model delta sigma weight residual 120.20 127.44 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" O3' G B 97 " pdb=" C3' G B 97 " pdb=" C2' G B 97 " ideal model delta sigma weight residual 109.50 116.42 -6.92 1.50e+00 4.44e-01 2.13e+01 ... (remaining 17742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 7052 34.86 - 69.71: 493 69.71 - 104.57: 46 104.57 - 139.42: 2 139.42 - 174.28: 2 Dihedral angle restraints: 7595 sinusoidal: 4399 harmonic: 3196 Sorted by residual: dihedral pdb=" O4' A B 98 " pdb=" C2' A B 98 " pdb=" C1' A B 98 " pdb=" C3' A B 98 " ideal model delta sinusoidal sigma weight residual 25.00 -13.57 38.57 1 8.00e+00 1.56e-02 3.27e+01 dihedral pdb=" C4' A B 98 " pdb=" O4' A B 98 " pdb=" C1' A B 98 " pdb=" C2' A B 98 " ideal model delta sinusoidal sigma weight residual 3.00 -30.59 33.59 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 18.39 86.20 1 2.00e+01 2.50e-03 2.24e+01 ... (remaining 7592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1960 0.112 - 0.225: 77 0.225 - 0.337: 7 0.337 - 0.449: 0 0.449 - 0.562: 1 Chirality restraints: 2045 Sorted by residual: chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2042 not shown) Planarity restraints: 1743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1128 " -0.021 2.00e-02 2.50e+03 3.62e-02 3.27e+01 pdb=" CG TRP A1128 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A1128 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A1128 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A1128 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A1128 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1128 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1128 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1128 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A1128 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 97 " -0.020 2.00e-02 2.50e+03 3.05e-02 2.78e+01 pdb=" N9 G B 97 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 97 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 97 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B 97 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 97 " 0.056 2.00e-02 2.50e+03 pdb=" O6 G B 97 " -0.054 2.00e-02 2.50e+03 pdb=" N1 G B 97 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 97 " 0.041 2.00e-02 2.50e+03 pdb=" N2 G B 97 " -0.034 2.00e-02 2.50e+03 pdb=" N3 G B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G B 97 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 88 " 0.044 2.00e-02 2.50e+03 3.33e-02 2.50e+01 pdb=" N1 C B 88 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C B 88 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C B 88 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C B 88 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C B 88 " -0.028 2.00e-02 2.50e+03 pdb=" N4 C B 88 " 0.025 2.00e-02 2.50e+03 pdb=" C5 C B 88 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C B 88 " -0.001 2.00e-02 2.50e+03 ... (remaining 1740 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 244 2.58 - 3.16: 9289 3.16 - 3.74: 23681 3.74 - 4.32: 32009 4.32 - 4.90: 47097 Nonbonded interactions: 112320 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1203 " model vdw 2.000 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 204 " model vdw 2.002 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.015 2.170 nonbonded pdb=" OP3 DT D 28 " pdb="MG MG A1203 " model vdw 2.025 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.030 2.170 ... (remaining 112315 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=0.00 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: 2.110 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 45.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 12555 Z= 0.391 Angle : 0.908 12.468 17747 Z= 0.481 Chirality : 0.054 0.562 2045 Planarity : 0.008 0.081 1743 Dihedral : 20.179 174.276 5521 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: -0.18 (0.23), residues: 1097 helix: 0.16 (0.21), residues: 539 sheet: -0.31 (0.56), residues: 82 loop : -0.24 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP A1128 HIS 0.007 0.002 HIS A 946 PHE 0.072 0.004 PHE A 363 TYR 0.019 0.003 TYR A 986 ARG 0.017 0.001 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.165 Fit side-chains REVERT: A 311 ASN cc_start: 0.7667 (m-40) cc_final: 0.7338 (m-40) REVERT: A 358 SER cc_start: 0.7626 (m) cc_final: 0.7420 (m) REVERT: A 720 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6494 (ttp-170) REVERT: A 723 ASP cc_start: 0.5636 (m-30) cc_final: 0.5329 (m-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.9771 time to fit residues: 242.9799 Evaluate side-chains 90 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.0050 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12555 Z= 0.324 Angle : 0.659 9.122 17747 Z= 0.345 Chirality : 0.043 0.307 2045 Planarity : 0.006 0.066 1743 Dihedral : 21.488 177.496 3432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.31 % Allowed : 6.67 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.59 (0.24), residues: 1097 helix: 0.95 (0.22), residues: 543 sheet: -0.35 (0.54), residues: 87 loop : 0.03 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1128 HIS 0.007 0.001 HIS A 603 PHE 0.024 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.007 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.100 Fit side-chains REVERT: A 311 ASN cc_start: 0.7667 (m-40) cc_final: 0.7224 (m-40) REVERT: A 548 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: A 602 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7341 (mtm-85) REVERT: A 720 ARG cc_start: 0.7016 (ttp-170) cc_final: 0.6425 (ttp-170) REVERT: A 724 ILE cc_start: 0.7398 (mm) cc_final: 0.7067 (mt) REVERT: A 1025 ASP cc_start: 0.6465 (t0) cc_final: 0.6261 (t70) outliers start: 12 outliers final: 4 residues processed: 100 average time/residue: 1.9824 time to fit residues: 210.1502 Evaluate side-chains 95 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12555 Z= 0.429 Angle : 0.729 9.570 17747 Z= 0.380 Chirality : 0.047 0.246 2045 Planarity : 0.007 0.071 1743 Dihedral : 21.541 177.508 3432 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 7.87 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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 (0.24), residues: 1097 helix: 0.95 (0.22), residues: 545 sheet: -0.48 (0.54), residues: 87 loop : 0.06 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 13 HIS 0.007 0.002 HIS A 603 PHE 0.023 0.003 PHE A 282 TYR 0.023 0.003 TYR A 986 ARG 0.009 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7585 (m-40) cc_final: 0.7158 (m-40) REVERT: A 602 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7580 (mtt-85) REVERT: A 662 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7311 (mtpt) REVERT: A 720 ARG cc_start: 0.7078 (ttp-170) cc_final: 0.6496 (ttp-170) REVERT: A 747 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: A 1025 ASP cc_start: 0.6493 (t0) cc_final: 0.6225 (t0) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 1.8736 time to fit residues: 203.1173 Evaluate side-chains 99 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12555 Z= 0.317 Angle : 0.649 9.515 17747 Z= 0.339 Chirality : 0.042 0.231 2045 Planarity : 0.006 0.062 1743 Dihedral : 21.450 176.039 3432 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 9.18 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.81 (0.25), residues: 1097 helix: 1.16 (0.22), residues: 547 sheet: -0.50 (0.58), residues: 76 loop : 0.12 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.022 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7570 (m-40) cc_final: 0.7121 (m-40) REVERT: A 662 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7299 (mtpt) REVERT: A 720 ARG cc_start: 0.7023 (ttp-170) cc_final: 0.6447 (ttp-170) REVERT: A 747 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7318 (mtp85) outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 1.9223 time to fit residues: 204.5064 Evaluate side-chains 93 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12555 Z= 0.340 Angle : 0.663 9.504 17747 Z= 0.346 Chirality : 0.043 0.227 2045 Planarity : 0.006 0.061 1743 Dihedral : 21.455 176.397 3432 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.64 % Allowed : 10.38 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.85 (0.25), residues: 1097 helix: 1.21 (0.22), residues: 545 sheet: -0.52 (0.58), residues: 76 loop : 0.13 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.022 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.6463 (mtt180) REVERT: A 311 ASN cc_start: 0.7599 (m-40) cc_final: 0.7076 (m-40) REVERT: A 662 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7307 (mtpt) REVERT: A 720 ARG cc_start: 0.7036 (ttp-170) cc_final: 0.6513 (ttp-170) REVERT: A 747 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7172 (mtp85) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 1.8930 time to fit residues: 197.0023 Evaluate side-chains 96 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 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 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12555 Z= 0.364 Angle : 0.677 9.525 17747 Z= 0.353 Chirality : 0.044 0.229 2045 Planarity : 0.006 0.064 1743 Dihedral : 21.474 176.400 3432 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.86 % Allowed : 11.26 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.79 (0.24), residues: 1097 helix: 1.20 (0.22), residues: 544 sheet: -0.69 (0.54), residues: 82 loop : 0.10 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 13 HIS 0.005 0.001 HIS A 749 PHE 0.022 0.002 PHE A 282 TYR 0.022 0.002 TYR A 986 ARG 0.005 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.180 Fit side-chains REVERT: A 137 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.6470 (mtt180) REVERT: A 217 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 311 ASN cc_start: 0.7595 (m-40) cc_final: 0.7054 (m-40) REVERT: A 548 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: A 662 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7305 (mtpt) REVERT: A 720 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6543 (ttp-170) REVERT: A 747 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: A 847 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7567 (mm-30) outliers start: 17 outliers final: 8 residues processed: 99 average time/residue: 1.8899 time to fit residues: 199.1765 Evaluate side-chains 97 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12555 Z= 0.196 Angle : 0.568 9.335 17747 Z= 0.297 Chirality : 0.038 0.223 2045 Planarity : 0.004 0.052 1743 Dihedral : 21.348 174.455 3432 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.31 % Allowed : 11.91 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.19 (0.25), residues: 1097 helix: 1.57 (0.22), residues: 545 sheet: -0.55 (0.57), residues: 76 loop : 0.22 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 603 PHE 0.018 0.002 PHE A 282 TYR 0.016 0.002 TYR A 986 ARG 0.006 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.6400 (mtt180) REVERT: A 311 ASN cc_start: 0.7563 (m-40) cc_final: 0.7060 (m-40) REVERT: A 630 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6514 (m-40) REVERT: A 654 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7010 (mtp-110) REVERT: A 662 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7294 (mtpt) REVERT: A 747 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7068 (mtp85) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 1.9533 time to fit residues: 198.9177 Evaluate side-chains 96 residues out of total 915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6008 > 50: distance: 62 - 70: 26.141 distance: 70 - 71: 22.535 distance: 71 - 72: 30.270 distance: 71 - 74: 44.567 distance: 72 - 73: 23.643 distance: 72 - 77: 39.960 distance: 74 - 75: 40.876 distance: 74 - 76: 9.346 distance: 77 - 78: 24.822 distance: 78 - 79: 28.218 distance: 78 - 81: 14.436 distance: 79 - 80: 24.218 distance: 79 - 82: 13.490 distance: 82 - 83: 17.274 distance: 83 - 84: 31.341 distance: 83 - 86: 21.885 distance: 84 - 85: 20.721 distance: 84 - 90: 25.139 distance: 86 - 87: 13.999 distance: 87 - 88: 29.489 distance: 87 - 89: 12.563 distance: 90 - 91: 48.597 distance: 91 - 92: 35.074 distance: 92 - 93: 38.600 distance: 92 - 94: 30.381 distance: 94 - 95: 12.270 distance: 95 - 96: 29.800 distance: 95 - 98: 14.719 distance: 96 - 97: 41.675 distance: 96 - 103: 32.593 distance: 98 - 99: 30.149 distance: 99 - 100: 20.043 distance: 100 - 101: 19.349 distance: 100 - 102: 14.058 distance: 103 - 104: 42.359 distance: 103 - 109: 39.896 distance: 104 - 105: 60.945 distance: 104 - 107: 40.676 distance: 105 - 106: 43.835 distance: 105 - 110: 42.345 distance: 107 - 108: 22.855 distance: 108 - 109: 33.885 distance: 110 - 111: 38.223 distance: 111 - 112: 18.360 distance: 111 - 114: 27.647 distance: 112 - 113: 8.226 distance: 112 - 121: 18.182 distance: 114 - 115: 9.270 distance: 115 - 116: 8.135 distance: 116 - 117: 9.481 distance: 117 - 118: 4.319 distance: 118 - 119: 6.078 distance: 118 - 120: 9.149 distance: 121 - 122: 12.613 distance: 122 - 123: 17.027 distance: 122 - 125: 9.064 distance: 123 - 124: 13.705 distance: 123 - 135: 18.634 distance: 125 - 126: 11.069 distance: 126 - 127: 21.311 distance: 126 - 128: 14.736 distance: 127 - 129: 18.251 distance: 128 - 130: 35.357 distance: 128 - 131: 11.290 distance: 129 - 130: 31.541 distance: 130 - 132: 21.350 distance: 131 - 133: 7.504 distance: 132 - 134: 6.527 distance: 133 - 134: 7.768 distance: 135 - 136: 13.447 distance: 136 - 137: 33.011 distance: 136 - 139: 21.164 distance: 137 - 138: 36.551 distance: 137 - 146: 38.947 distance: 139 - 140: 21.928 distance: 140 - 141: 15.380 distance: 141 - 142: 12.997 distance: 142 - 143: 8.842 distance: 143 - 144: 8.670 distance: 143 - 145: 11.160 distance: 146 - 147: 39.177 distance: 147 - 148: 32.054 distance: 147 - 150: 12.480 distance: 148 - 149: 19.425 distance: 148 - 157: 13.946 distance: 150 - 151: 41.470 distance: 151 - 152: 24.990 distance: 152 - 153: 23.245 distance: 153 - 154: 15.311 distance: 154 - 155: 15.921 distance: 154 - 156: 13.200