Starting phenix.real_space_refine on Fri Aug 2 14:57:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/08_2024/8ve5_43165.cif" } resolution = 3.4 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= 0.002 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 S 3 5.16 5 Cl 2 4.86 5 C 2201 2.51 5 N 576 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3382 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 860 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 837 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 827 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 839 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'P2C': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.77, per 1000 atoms: 0.82 Number of scatterers: 3382 At special positions: 0 Unit cell: (76.994, 67.44, 60.696, 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) Cl 2 17.00 S 3 16.00 O 600 8.00 N 576 7.00 C 2201 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: 1.34 Conformation dependent library (CDL) restraints added in 758.7 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 7.1% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.788A pdb=" N LEU A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.751A pdb=" N LEU B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.674A pdb=" N TRP C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 82 removed outlier: 3.635A pdb=" N LYS D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.649A pdb=" N VAL A 14 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.649A pdb=" N VAL A 14 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 5.470A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 29 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 94 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N GLU B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N HIS B 90 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 95 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS B 88 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.007A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 119 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 110 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 119 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.473A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 29 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 70 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 95 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS C 88 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE D 95 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS C 90 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLU C 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA D 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 94 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 67 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 30 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER D 46 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 32 " --> pdb=" O PHE D 44 " (cutoff:3.500A) 141 hydrogen bonds defined for protein. 396 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: 0.82 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1070 1.34 - 1.46: 853 1.46 - 1.57: 1547 1.57 - 1.69: 1 1.69 - 1.81: 7 Bond restraints: 3478 Sorted by residual: bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.40e+00 bond pdb=" C5 P2C B 201 " pdb=" N18 P2C B 201 " ideal model delta sigma weight residual 1.361 1.402 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C13 P2C B 201 " pdb=" C19 P2C B 201 " ideal model delta sigma weight residual 1.527 1.497 0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" CB VAL D 16 " pdb=" CG1 VAL D 16 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.36e-01 bond pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 1.466 1.453 0.013 1.50e-02 4.44e+03 7.39e-01 ... (remaining 3473 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 122 106.17 - 113.12: 1913 113.12 - 120.08: 1071 120.08 - 127.03: 1611 127.03 - 133.99: 55 Bond angle restraints: 4772 Sorted by residual: angle pdb=" CA PRO C 125 " pdb=" N PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 112.00 105.60 6.40 1.40e+00 5.10e-01 2.09e+01 angle pdb=" N PRO C 125 " pdb=" CD PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 103.20 99.21 3.99 1.50e+00 4.44e-01 7.07e+00 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.40e+00 angle pdb=" N PHE A 44 " pdb=" CA PHE A 44 " pdb=" C PHE A 44 " ideal model delta sigma weight residual 113.18 110.11 3.07 1.33e+00 5.65e-01 5.32e+00 angle pdb=" CB LYS D 15 " pdb=" CG LYS D 15 " pdb=" CD LYS D 15 " ideal model delta sigma weight residual 111.30 106.49 4.81 2.30e+00 1.89e-01 4.38e+00 ... (remaining 4767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 1866 16.04 - 32.08: 108 32.08 - 48.12: 23 48.12 - 64.16: 4 64.16 - 80.20: 3 Dihedral angle restraints: 2004 sinusoidal: 644 harmonic: 1360 Sorted by residual: dihedral pdb=" CA PRO B 86 " pdb=" C PRO B 86 " pdb=" N PHE B 87 " pdb=" CA PHE B 87 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA SER A 23 " pdb=" C SER A 23 " pdb=" N PRO A 24 " pdb=" CA PRO A 24 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU A 72 " pdb=" CG GLU A 72 " pdb=" CD GLU A 72 " pdb=" OE1 GLU A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -80.20 80.20 1 3.00e+01 1.11e-03 8.85e+00 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 282 0.027 - 0.053: 156 0.053 - 0.079: 42 0.079 - 0.106: 42 0.106 - 0.132: 32 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE B 84 " pdb=" N ILE B 84 " pdb=" C ILE B 84 " pdb=" CB ILE B 84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 551 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 102 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 86 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 23 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO B 24 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.018 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 418 2.75 - 3.29: 3069 3.29 - 3.83: 5484 3.83 - 4.36: 6079 4.36 - 4.90: 11549 Nonbonded interactions: 26599 Sorted by model distance: nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP B 18 " pdb=" NH2 ARG B 21 " model vdw 2.327 3.120 nonbonded pdb=" OD2 ASP B 18 " pdb=" OH TYR B 78 " model vdw 2.330 3.040 nonbonded pdb=" O PHE B 64 " pdb=" ND2 ASN B 98 " model vdw 2.332 3.120 nonbonded pdb=" O THR C 60 " pdb=" N PHE C 64 " model vdw 2.374 3.120 ... (remaining 26594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 25 or (resid 26 throu \ gh 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throu \ gh 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ me CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or \ name O or name CB )) or (resid 53 through 56 and (name N or name CA or name C o \ r name O or name CB )) or resid 57 through 58 or (resid 59 through 63 and (name \ N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 through \ 66 and (name N or name CA or name C or name O or name CB )) or resid 67 through \ 68 or (resid 69 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 70 throu \ gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ esid 75 or (resid 76 through 77 and (name N or name CA or name C or name O or na \ me CB )) or resid 78 through 79 or (resid 80 through 81 and (name N or name CA o \ r name C or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N \ or name CA or name C or name O or name CB )) or resid 86 through 88 or (resid 8 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 90 through 9 \ 1 or (resid 92 and (name N or name CA or name C or name O or name CB )) or resid \ 93 through 98 or (resid 99 through 100 and (name N or name CA or name C or name \ O or name CB )) or resid 101 through 102 or (resid 103 through 104 and (name N \ or name CA or name C or name O or name CB )) or resid 105 or (resid 106 and (nam \ e N or name CA or name C or name O or name CB )) or resid 107 through 111 or (re \ sid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 th \ rough 114 or (resid 115 and (name N or name CA or name C or name O or name CB )) \ or resid 116 or (resid 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 or (resid 119 through 120 and (name N or name CA or name C or \ name O or name CB )) or resid 121 through 122 or (resid 123 through 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125)) selection = (chain 'B' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name \ O or name CB )) or resid 16 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 25 or (resid 26 through 27 and \ (name N or name CA or name C or name O or name CB )) or resid 28 through 33 or ( \ resid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 th \ rough 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) o \ r resid 47 or (resid 48 through 49 and (name N or name CA or name C or name O or \ name CB )) or resid 50 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 or (resid 54 through 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 throug \ h 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 68 or (resid 69 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 70 thr \ ough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 84 or (resid 85 and (name N or name CA or name C or name O or \ name CB )) or resid 86 through 102 or (resid 103 through 104 and (name N or name \ CA or name C or name O or name CB )) or resid 105 or (resid 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 116 or (resid 117 \ and (name N or name CA or name C or name O or name CB )) or resid 118 or (resid \ 119 through 120 and (name N or name CA or name C or name O or name CB )) or res \ id 121 through 123 or (resid 124 and (name N or name CA or name C or name O or n \ ame CB )) or resid 125)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 or (resid 15 and (name N or name CA or nam \ e C or name O or name CB )) or resid 16 through 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 25 or (resid 26 thr \ ough 27 and (name N or name CA or name C or name O or name CB )) or resid 28 thr \ ough 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or \ resid 35 through 41 or (resid 42 and (name N or name CA or name C or name O or \ name CB )) or resid 43 through 47 or (resid 48 through 49 and (name N or name CA \ or name C or name O or name CB )) or resid 50 through 54 or (resid 55 through 5 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 57 through 6 \ 0 or (resid 61 through 63 and (name N or name CA or name C or name O or name CB \ )) or resid 64 through 68 or (resid 69 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 70 through 75 or (resid 76 through 77 and (name N or name CA or n \ ame C or name O or name CB )) or resid 78 through 79 or (resid 80 through 81 and \ (name N or name CA or name C or name O or name CB )) or resid 82 through 88 or \ (resid 89 and (name N or name CA or name C or name O or name CB )) or resid 90 t \ hrough 98 or (resid 99 through 100 and (name N or name CA or name C or name O or \ name CB )) or resid 101 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB )) or resid 105 through 125)) selection = (chain 'D' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 through 37 or (resid 38 throu \ gh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 throu \ gh 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or n \ ame O or name CB )) or resid 53 or (resid 54 through 56 and (name N or name CA o \ r name C or name O or name CB )) or resid 57 through 58 or (resid 59 through 63 \ and (name N or name CA or name C or name O or name CB )) or resid 64 through 75 \ or (resid 76 through 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 79 or (resid 80 through 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N or name \ CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 thro \ ugh 104 and (name N or name CA or name C or name O or name CB )) or resid 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 7 through 111 or (resid 112 and (name N or name CA or name C or name O or name C \ B )) or resid 113 through 114 or (resid 115 and (name N or name CA or name C or \ name O or name CB )) or resid 116 or (resid 117 and (name N or name CA or name C \ or name O or name CB )) or resid 118 through 125)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.005 0.116 3478 Z= 0.315 Angle : 0.584 8.050 4772 Z= 0.309 Chirality : 0.048 0.132 554 Planarity : 0.005 0.055 605 Dihedral : 11.514 80.199 1126 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.41), residues: 459 helix: -0.84 (0.87), residues: 28 sheet: 0.80 (0.38), residues: 229 loop : 0.26 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.002 0.001 HIS C 31 PHE 0.019 0.002 PHE B 44 TYR 0.013 0.002 TYR A 69 ARG 0.006 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.5984 (ttp) cc_final: 0.5585 (tmm) REVERT: A 14 VAL cc_start: 0.8843 (t) cc_final: 0.8503 (p) REVERT: A 103 ARG cc_start: 0.7416 (mpt180) cc_final: 0.6898 (mmt-90) REVERT: A 117 SER cc_start: 0.9277 (t) cc_final: 0.9075 (t) REVERT: C 13 MET cc_start: 0.6619 (tmm) cc_final: 0.6302 (ptm) REVERT: C 35 LYS cc_start: 0.7756 (tptt) cc_final: 0.7145 (tppt) REVERT: D 103 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7058 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2077 time to fit residues: 19.0847 Evaluate side-chains 66 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3478 Z= 0.206 Angle : 0.549 7.138 4772 Z= 0.289 Chirality : 0.049 0.144 554 Planarity : 0.005 0.046 605 Dihedral : 4.032 20.369 498 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.97 % Allowed : 7.92 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.41), residues: 459 helix: -0.71 (0.86), residues: 28 sheet: 1.14 (0.37), residues: 228 loop : -0.03 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.002 0.001 HIS A 56 PHE 0.008 0.001 PHE D 44 TYR 0.011 0.001 TYR D 116 ARG 0.006 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6219 (ttp) cc_final: 0.5631 (tmm) REVERT: A 14 VAL cc_start: 0.9034 (t) cc_final: 0.8704 (p) REVERT: A 103 ARG cc_start: 0.7346 (mpt180) cc_final: 0.6738 (mmt-90) REVERT: C 13 MET cc_start: 0.6601 (tmm) cc_final: 0.6301 (ptm) REVERT: D 34 ARG cc_start: 0.7634 (ttt180) cc_final: 0.7394 (ttt180) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.1988 time to fit residues: 17.6936 Evaluate side-chains 72 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3478 Z= 0.344 Angle : 0.596 6.610 4772 Z= 0.315 Chirality : 0.050 0.152 554 Planarity : 0.005 0.043 605 Dihedral : 4.331 17.992 498 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.96 % Allowed : 8.91 % Favored : 87.13 % 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: 0.33 (0.41), residues: 459 helix: -1.23 (0.79), residues: 34 sheet: 0.77 (0.37), residues: 228 loop : -0.05 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 79 HIS 0.003 0.001 HIS C 88 PHE 0.012 0.002 PHE C 44 TYR 0.011 0.002 TYR D 116 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6342 (ttp) cc_final: 0.5745 (tmm) REVERT: A 14 VAL cc_start: 0.9035 (t) cc_final: 0.8664 (p) REVERT: A 103 ARG cc_start: 0.7288 (mpt180) cc_final: 0.6746 (mmt-90) REVERT: C 13 MET cc_start: 0.6518 (tmm) cc_final: 0.6252 (ptm) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.2080 time to fit residues: 17.8601 Evaluate side-chains 70 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3478 Z= 0.278 Angle : 0.566 6.887 4772 Z= 0.298 Chirality : 0.049 0.149 554 Planarity : 0.005 0.040 605 Dihedral : 4.189 18.547 498 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.96 % Allowed : 11.88 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.41), residues: 459 helix: -1.18 (0.82), residues: 34 sheet: 0.65 (0.37), residues: 229 loop : -0.04 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.002 0.001 HIS C 88 PHE 0.010 0.001 PHE C 44 TYR 0.017 0.002 TYR C 78 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6316 (ttp) cc_final: 0.5731 (tmm) REVERT: A 14 VAL cc_start: 0.9027 (t) cc_final: 0.8647 (p) REVERT: A 103 ARG cc_start: 0.7233 (mpt180) cc_final: 0.6921 (mmt-90) REVERT: C 13 MET cc_start: 0.6557 (tmm) cc_final: 0.6258 (ptm) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.2254 time to fit residues: 18.5612 Evaluate side-chains 70 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3478 Z= 0.301 Angle : 0.573 6.874 4772 Z= 0.302 Chirality : 0.049 0.150 554 Planarity : 0.005 0.040 605 Dihedral : 4.224 18.457 498 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.96 % Allowed : 12.54 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.41), residues: 459 helix: -1.15 (0.82), residues: 34 sheet: 0.48 (0.37), residues: 223 loop : -0.17 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS B 31 PHE 0.011 0.001 PHE C 44 TYR 0.021 0.002 TYR C 78 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6365 (ttp) cc_final: 0.5773 (tmm) REVERT: A 14 VAL cc_start: 0.9036 (t) cc_final: 0.8647 (p) REVERT: A 103 ARG cc_start: 0.7212 (mpt180) cc_final: 0.6916 (mmt-90) REVERT: C 13 MET cc_start: 0.6547 (tmm) cc_final: 0.6242 (ptm) REVERT: C 15 LYS cc_start: 0.8128 (tmtt) cc_final: 0.7629 (tmtt) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.2031 time to fit residues: 16.6699 Evaluate side-chains 75 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 31 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3478 Z= 0.186 Angle : 0.522 6.668 4772 Z= 0.271 Chirality : 0.047 0.141 554 Planarity : 0.005 0.041 605 Dihedral : 3.925 20.232 498 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.30 % Allowed : 13.86 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.40), residues: 459 helix: -1.27 (0.81), residues: 34 sheet: 0.65 (0.37), residues: 223 loop : -0.23 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.002 0.001 HIS B 88 PHE 0.006 0.001 PHE D 87 TYR 0.017 0.001 TYR C 105 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6342 (ttp) cc_final: 0.5786 (tmm) REVERT: A 14 VAL cc_start: 0.9016 (t) cc_final: 0.8634 (p) REVERT: A 103 ARG cc_start: 0.7140 (mpt180) cc_final: 0.6553 (mmt-90) REVERT: C 13 MET cc_start: 0.6664 (tmm) cc_final: 0.6343 (ptm) REVERT: C 15 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7569 (tmtt) REVERT: D 105 TYR cc_start: 0.8564 (m-80) cc_final: 0.8189 (m-10) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.2100 time to fit residues: 18.1076 Evaluate side-chains 73 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3478 Z= 0.262 Angle : 0.560 6.530 4772 Z= 0.293 Chirality : 0.048 0.147 554 Planarity : 0.005 0.040 605 Dihedral : 4.012 19.778 498 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.30 % Allowed : 15.84 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.41), residues: 459 helix: -1.30 (0.82), residues: 34 sheet: 0.57 (0.37), residues: 223 loop : -0.27 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.002 0.001 HIS C 88 PHE 0.008 0.001 PHE C 44 TYR 0.012 0.002 TYR C 105 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6374 (ttp) cc_final: 0.5807 (tmm) REVERT: A 14 VAL cc_start: 0.9028 (t) cc_final: 0.8644 (p) REVERT: A 103 ARG cc_start: 0.7161 (mpt180) cc_final: 0.6849 (mmt-90) REVERT: C 13 MET cc_start: 0.6641 (tmm) cc_final: 0.6311 (ptm) REVERT: C 15 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7625 (tmtt) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.2065 time to fit residues: 16.3303 Evaluate side-chains 71 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3478 Z= 0.290 Angle : 0.575 6.569 4772 Z= 0.301 Chirality : 0.049 0.148 554 Planarity : 0.005 0.042 605 Dihedral : 4.136 19.695 498 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.29 % Allowed : 16.17 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.41), residues: 459 helix: -1.32 (0.82), residues: 34 sheet: 0.47 (0.37), residues: 223 loop : -0.27 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.002 0.001 HIS B 31 PHE 0.009 0.001 PHE C 44 TYR 0.019 0.002 TYR C 105 ARG 0.008 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6397 (ttp) cc_final: 0.5944 (tmm) REVERT: A 14 VAL cc_start: 0.9053 (t) cc_final: 0.8634 (m) REVERT: A 103 ARG cc_start: 0.7159 (mpt180) cc_final: 0.6551 (mmt-90) REVERT: C 13 MET cc_start: 0.6623 (tmm) cc_final: 0.6293 (ptm) REVERT: C 15 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7626 (tmtt) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.2330 time to fit residues: 18.0047 Evaluate side-chains 70 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3478 Z= 0.174 Angle : 0.529 6.645 4772 Z= 0.275 Chirality : 0.047 0.141 554 Planarity : 0.005 0.051 605 Dihedral : 3.850 21.019 498 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 17.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.41), residues: 459 helix: -1.28 (0.85), residues: 34 sheet: 0.70 (0.38), residues: 223 loop : -0.32 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 79 HIS 0.002 0.001 HIS B 88 PHE 0.007 0.001 PHE C 87 TYR 0.018 0.001 TYR C 105 ARG 0.007 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6362 (ttp) cc_final: 0.5796 (tmm) REVERT: A 14 VAL cc_start: 0.9029 (t) cc_final: 0.8645 (p) REVERT: A 103 ARG cc_start: 0.7099 (mpt180) cc_final: 0.6780 (mmt-90) REVERT: C 13 MET cc_start: 0.6689 (tmm) cc_final: 0.6279 (ptm) REVERT: C 15 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7544 (tmtt) REVERT: D 105 TYR cc_start: 0.8536 (m-80) cc_final: 0.8130 (m-10) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.2194 time to fit residues: 17.7514 Evaluate side-chains 67 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3478 Z= 0.143 Angle : 0.510 6.729 4772 Z= 0.264 Chirality : 0.047 0.134 554 Planarity : 0.005 0.054 605 Dihedral : 3.559 21.647 498 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.31 % Allowed : 18.81 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.41), residues: 459 helix: -1.35 (0.82), residues: 34 sheet: 0.93 (0.38), residues: 223 loop : -0.34 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.002 0.000 HIS D 56 PHE 0.008 0.001 PHE C 87 TYR 0.016 0.001 TYR C 105 ARG 0.007 0.000 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6283 (ttp) cc_final: 0.5895 (tmm) REVERT: A 103 ARG cc_start: 0.7058 (mpt180) cc_final: 0.6481 (mmt-90) REVERT: C 15 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7501 (tmtt) outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 0.2191 time to fit residues: 17.2200 Evaluate side-chains 70 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122142 restraints weight = 4682.393| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.50 r_work: 0.3478 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3478 Z= 0.233 Angle : 0.555 6.533 4772 Z= 0.290 Chirality : 0.048 0.141 554 Planarity : 0.005 0.048 605 Dihedral : 3.801 19.032 498 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.64 % Allowed : 19.47 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.41), residues: 459 helix: -1.37 (0.83), residues: 34 sheet: 0.95 (0.38), residues: 220 loop : -0.39 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.002 0.001 HIS C 88 PHE 0.007 0.001 PHE C 44 TYR 0.017 0.002 TYR B 116 ARG 0.007 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.23 seconds wall clock time: 22 minutes 20.08 seconds (1340.08 seconds total)