Starting phenix.real_space_refine on Thu Feb 15 02:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1j_32943/02_2024/7x1j_32943_neut_updated.pdb" } resolution = 2.84 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= 0.028 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 6 5.49 5 S 62 5.16 5 C 7184 2.51 5 N 1782 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10928 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5409 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 648} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5409 Classifications: {'peptide': 678} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 648} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.05, per 1000 atoms: 0.55 Number of scatterers: 10928 At special positions: 0 Unit cell: (84.563, 125.613, 110.014, 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 62 16.00 P 6 15.00 O 1894 8.00 N 1782 7.00 C 7184 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: 7.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 4 sheets defined 61.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.538A pdb=" N PHE B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.994A pdb=" N PHE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 401 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 488 through 516 removed outlier: 4.056A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.167A pdb=" N LYS B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 658 through 683 Processing helix chain 'B' and resid 696 through 712 Processing helix chain 'B' and resid 722 through 732 Proline residue: B 726 - end of helix Processing helix chain 'B' and resid 756 through 769 removed outlier: 3.686A pdb=" N LEU B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 778 Processing helix chain 'B' and resid 781 through 796 removed outlier: 3.654A pdb=" N LEU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 826 through 847 Processing helix chain 'B' and resid 852 through 870 Proline residue: B 859 - end of helix removed outlier: 4.126A pdb=" N ILE B 866 " --> pdb=" O MET B 862 " (cutoff:3.500A) Proline residue: B 867 - end of helix Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.614A pdb=" N ILE B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 879 through 886 Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.538A pdb=" N PHE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.994A pdb=" N PHE A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 401 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 456 through 476 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 488 through 516 removed outlier: 4.056A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 596 removed outlier: 4.167A pdb=" N LYS A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 658 through 683 Processing helix chain 'A' and resid 696 through 712 Processing helix chain 'A' and resid 722 through 732 Proline residue: A 726 - end of helix Processing helix chain 'A' and resid 756 through 769 removed outlier: 3.686A pdb=" N LEU A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 778 Processing helix chain 'A' and resid 781 through 796 removed outlier: 3.654A pdb=" N LEU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 826 through 847 Processing helix chain 'A' and resid 852 through 870 Proline residue: A 859 - end of helix removed outlier: 4.126A pdb=" N ILE A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.614A pdb=" N ILE A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 876' Processing helix chain 'A' and resid 879 through 886 Processing sheet with id= A, first strand: chain 'B' and resid 138 through 140 removed outlier: 4.334A pdb=" N SER B 138 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 255 " --> pdb=" O CYS B 219 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 196 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.036A pdb=" N ASN B 750 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 736 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 748 " --> pdb=" O GLU B 736 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 138 through 140 removed outlier: 4.335A pdb=" N SER A 138 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 255 " --> pdb=" O CYS A 219 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP A 196 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.036A pdb=" N ASN A 750 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU A 736 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE A 748 " --> pdb=" O GLU A 736 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1727 1.32 - 1.44: 2923 1.44 - 1.57: 6412 1.57 - 1.69: 8 1.69 - 1.81: 102 Bond restraints: 11172 Sorted by residual: bond pdb=" C19 PT5 B2000 " pdb=" C20 PT5 B2000 " ideal model delta sigma weight residual 1.588 1.316 0.272 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C19 PT5 A2000 " pdb=" C20 PT5 A2000 " ideal model delta sigma weight residual 1.588 1.316 0.272 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C21 PT5 A2000 " pdb=" C22 PT5 A2000 " ideal model delta sigma weight residual 1.361 1.526 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C21 PT5 B2000 " pdb=" C22 PT5 B2000 " ideal model delta sigma weight residual 1.361 1.526 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C24 PT5 B2000 " pdb=" C25 PT5 B2000 " ideal model delta sigma weight residual 1.357 1.520 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 11167 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.42: 387 107.42 - 114.46: 6733 114.46 - 121.51: 5781 121.51 - 128.56: 2151 128.56 - 135.61: 98 Bond angle restraints: 15150 Sorted by residual: angle pdb=" C18 PT5 B2000 " pdb=" C19 PT5 B2000 " pdb=" C20 PT5 B2000 " ideal model delta sigma weight residual 85.86 126.31 -40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C18 PT5 A2000 " pdb=" C19 PT5 A2000 " pdb=" C20 PT5 A2000 " ideal model delta sigma weight residual 85.86 126.26 -40.40 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C15 PT5 A2000 " pdb=" C16 PT5 A2000 " pdb=" C17 PT5 A2000 " ideal model delta sigma weight residual 152.67 113.75 38.92 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C15 PT5 B2000 " pdb=" C16 PT5 B2000 " pdb=" C17 PT5 B2000 " ideal model delta sigma weight residual 152.67 113.77 38.90 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C21 PT5 B2000 " pdb=" C22 PT5 B2000 " pdb=" C23 PT5 B2000 " ideal model delta sigma weight residual 152.70 113.87 38.83 3.00e+00 1.11e-01 1.68e+02 ... (remaining 15145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 6596 33.47 - 66.95: 48 66.95 - 100.42: 4 100.42 - 133.89: 0 133.89 - 167.37: 4 Dihedral angle restraints: 6652 sinusoidal: 2678 harmonic: 3974 Sorted by residual: dihedral pdb=" C21 PT5 B2000 " pdb=" C22 PT5 B2000 " pdb=" C23 PT5 B2000 " pdb=" C24 PT5 B2000 " ideal model delta sinusoidal sigma weight residual 345.96 178.59 167.37 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C21 PT5 A2000 " pdb=" C22 PT5 A2000 " pdb=" C23 PT5 A2000 " pdb=" C24 PT5 A2000 " ideal model delta sinusoidal sigma weight residual 345.96 178.62 167.34 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C12 PT5 B2000 " pdb=" C13 PT5 B2000 " pdb=" C14 PT5 B2000 " pdb=" C15 PT5 B2000 " ideal model delta sinusoidal sigma weight residual 21.27 -130.35 151.62 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 6649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 1782 1.000 - 1.999: 0 1.999 - 2.999: 0 2.999 - 3.998: 0 3.998 - 4.998: 2 Chirality restraints: 1784 Sorted by residual: chirality pdb=" C2 PT5 B2000 " pdb=" C1 PT5 B2000 " pdb=" C3 PT5 B2000 " pdb=" O2 PT5 B2000 " both_signs ideal model delta sigma weight residual False -2.52 2.48 -5.00 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" C2 PT5 A2000 " pdb=" C1 PT5 A2000 " pdb=" C3 PT5 A2000 " pdb=" O2 PT5 A2000 " both_signs ideal model delta sigma weight residual False -2.52 2.48 -5.00 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" CA LEU B 600 " pdb=" N LEU B 600 " pdb=" C LEU B 600 " pdb=" CB LEU B 600 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 1781 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 PT5 A2000 " -0.030 2.00e-02 2.50e+03 2.56e-01 6.55e+02 pdb=" C18 PT5 A2000 " 0.226 2.00e-02 2.50e+03 pdb=" C19 PT5 A2000 " -0.407 2.00e-02 2.50e+03 pdb=" C20 PT5 A2000 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 PT5 B2000 " 0.030 2.00e-02 2.50e+03 2.56e-01 6.54e+02 pdb=" C18 PT5 B2000 " -0.225 2.00e-02 2.50e+03 pdb=" C19 PT5 B2000 " 0.407 2.00e-02 2.50e+03 pdb=" C20 PT5 B2000 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PT5 A2000 " -0.030 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C21 PT5 A2000 " 0.029 2.00e-02 2.50e+03 pdb=" C22 PT5 A2000 " 0.030 2.00e-02 2.50e+03 pdb=" C23 PT5 A2000 " -0.029 2.00e-02 2.50e+03 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2690 2.81 - 3.33: 11023 3.33 - 3.85: 18200 3.85 - 4.38: 22309 4.38 - 4.90: 37702 Nonbonded interactions: 91924 Sorted by model distance: nonbonded pdb=" O ILE B 498 " pdb=" OG1 THR B 501 " model vdw 2.284 2.440 nonbonded pdb=" O ILE A 498 " pdb=" OG1 THR A 501 " model vdw 2.285 2.440 nonbonded pdb=" O THR A 274 " pdb=" OG SER A 277 " model vdw 2.292 2.440 nonbonded pdb=" O THR B 274 " pdb=" OG SER B 277 " model vdw 2.293 2.440 nonbonded pdb=" NE2 GLN A 408 " pdb=" O ASN A 639 " model vdw 2.294 2.520 ... (remaining 91919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 13.530 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.530 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.007 0.272 11172 Z= 0.533 Angle : 1.024 40.454 15150 Z= 0.401 Chirality : 0.172 4.998 1784 Planarity : 0.009 0.256 1846 Dihedral : 10.581 167.368 4076 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.85 % Allowed : 1.02 % Favored : 98.13 % 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: 2.94 (0.23), residues: 1328 helix: 2.64 (0.17), residues: 878 sheet: 3.18 (0.52), residues: 76 loop : -0.03 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 717 HIS 0.002 0.000 HIS B 719 PHE 0.004 0.001 PHE B 832 TYR 0.007 0.001 TYR A 820 ARG 0.002 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.299 Fit side-chains REVERT: B 505 ASP cc_start: 0.7044 (m-30) cc_final: 0.6776 (m-30) REVERT: B 853 TYR cc_start: 0.6507 (m-80) cc_final: 0.6038 (m-80) REVERT: A 853 TYR cc_start: 0.6594 (m-80) cc_final: 0.6111 (m-80) outliers start: 10 outliers final: 6 residues processed: 221 average time/residue: 1.2175 time to fit residues: 289.1119 Evaluate side-chains 151 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 149 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS B 199 GLN B 225 GLN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 724 HIS ** B 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 199 GLN A 225 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 724 HIS ** A 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11172 Z= 0.317 Angle : 0.619 12.155 15150 Z= 0.295 Chirality : 0.044 0.183 1784 Planarity : 0.005 0.037 1846 Dihedral : 10.282 145.554 1534 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 8.23 % Favored : 89.39 % 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: 2.23 (0.23), residues: 1328 helix: 2.17 (0.17), residues: 860 sheet: 2.46 (0.53), residues: 76 loop : -0.28 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.006 0.002 HIS A 724 PHE 0.024 0.002 PHE B 620 TYR 0.009 0.001 TYR B 722 ARG 0.005 0.001 ARG A 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 304 LEU cc_start: 0.8749 (mp) cc_final: 0.8462 (mp) REVERT: A 304 LEU cc_start: 0.8797 (mp) cc_final: 0.8511 (mp) REVERT: A 793 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 28 outliers final: 13 residues processed: 169 average time/residue: 1.2517 time to fit residues: 226.3765 Evaluate side-chains 148 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 809 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 283 GLN B 300 HIS B 303 GLN B 639 ASN ** B 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 225 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 300 HIS A 639 ASN ** A 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11172 Z= 0.261 Angle : 0.562 12.911 15150 Z= 0.271 Chirality : 0.041 0.151 1784 Planarity : 0.005 0.044 1846 Dihedral : 9.431 117.443 1530 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.55 % Allowed : 9.08 % Favored : 88.37 % 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: 1.96 (0.22), residues: 1328 helix: 1.99 (0.17), residues: 862 sheet: 2.31 (0.53), residues: 76 loop : -0.46 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 462 HIS 0.005 0.001 HIS B 192 PHE 0.021 0.002 PHE B 620 TYR 0.010 0.001 TYR B 722 ARG 0.007 0.001 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 0.944 Fit side-chains REVERT: B 304 LEU cc_start: 0.8795 (mp) cc_final: 0.8472 (mp) REVERT: B 647 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6894 (tmm) REVERT: B 737 GLU cc_start: 0.7776 (tp30) cc_final: 0.7532 (tp30) REVERT: A 304 LEU cc_start: 0.8777 (mp) cc_final: 0.8440 (mp) outliers start: 30 outliers final: 16 residues processed: 160 average time/residue: 1.0400 time to fit residues: 179.0854 Evaluate side-chains 156 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 809 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 238 GLN B 283 GLN B 300 HIS B 601 HIS B 639 ASN ** B 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 225 GLN ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 300 HIS A 303 GLN A 601 HIS A 639 ASN ** A 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11172 Z= 0.243 Angle : 0.547 12.134 15150 Z= 0.265 Chirality : 0.041 0.152 1784 Planarity : 0.005 0.047 1846 Dihedral : 8.996 124.099 1530 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.46 % Allowed : 9.59 % Favored : 87.95 % 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: 1.83 (0.22), residues: 1328 helix: 1.88 (0.17), residues: 868 sheet: 1.75 (0.53), residues: 80 loop : -0.45 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 462 HIS 0.005 0.001 HIS B 192 PHE 0.020 0.001 PHE B 620 TYR 0.011 0.001 TYR B 722 ARG 0.010 0.001 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.951 Fit side-chains REVERT: B 259 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7785 (mmt) REVERT: B 647 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7005 (tmm) REVERT: A 259 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7783 (mmt) REVERT: A 823 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.7888 (mmt90) outliers start: 29 outliers final: 12 residues processed: 154 average time/residue: 1.0701 time to fit residues: 176.8127 Evaluate side-chains 147 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 647 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 809 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 110 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: