Starting phenix.real_space_refine on Mon Jun 24 16:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/06_2024/8ve5_43165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/06_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_43165/06_2024/8ve5_43165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/06_2024/8ve5_43165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/06_2024/8ve5_43165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve5_43165/06_2024/8ve5_43165_updated.pdb" } 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-5370/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: 2.88, per 1000 atoms: 0.85 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: 1.32 Conformation dependent library (CDL) restraints added in 662.5 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... running ksdssp... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.8% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 76 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 76 through 82 removed outlier: 3.751A pdb=" N LEU B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.737A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 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= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 7.314A pdb=" N TYR A 105 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LYS A 15 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 107 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LEU A 17 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 109 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 97 removed outlier: 5.046A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 29 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 12 through 18 removed outlier: 7.469A pdb=" N TYR B 105 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N LYS B 15 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 107 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LEU B 17 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 109 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 91 through 97 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= E, first strand: chain 'C' and resid 12 through 18 removed outlier: 7.215A pdb=" N TYR C 105 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LYS C 15 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 107 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LEU C 17 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 109 " --> pdb=" O LEU C 17 " (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) Processing sheet with id= F, first strand: chain 'C' and resid 90 through 97 removed outlier: 3.675A pdb=" N PHE C 95 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 70 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 29 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 12 through 18 removed outlier: 7.113A pdb=" N TYR D 105 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LYS D 15 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 107 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU D 17 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA D 109 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 119 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 91 through 97 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: 4.158A pdb=" N ALA D 29 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 276 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: 1.10 Time building geometry restraints manager: 1.46 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: 421 2.75 - 3.29: 3083 3.29 - 3.83: 5514 3.83 - 4.36: 6105 4.36 - 4.90: 11556 Nonbonded interactions: 26679 Sorted by model distance: nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.216 2.440 nonbonded pdb=" OD2 ASP B 18 " pdb=" NH2 ARG B 21 " model vdw 2.327 2.520 nonbonded pdb=" OD2 ASP B 18 " pdb=" OH TYR B 78 " model vdw 2.330 2.440 nonbonded pdb=" O PHE B 64 " pdb=" ND2 ASN B 98 " model vdw 2.332 2.520 nonbonded pdb=" O THR C 60 " pdb=" N PHE C 64 " model vdw 2.374 2.520 ... (remaining 26674 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' 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: 0.690 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: 3.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.310 Find NCS groups from input model: 0.240 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- 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= 0.299 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 : 0.399 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: 0.2115 time to fit residues: 19.3988 Evaluate side-chains 66 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 3478 Z= 0.153 Angle : 0.507 7.265 4772 Z= 0.261 Chirality : 0.047 0.142 554 Planarity : 0.005 0.045 605 Dihedral : 3.916 23.221 498 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.30 % Allowed : 7.92 % Favored : 88.78 % 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: 0.68 (0.41), residues: 459 helix: -1.38 (0.79), residues: 34 sheet: 1.20 (0.38), residues: 223 loop : 0.00 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.001 0.000 HIS A 31 PHE 0.007 0.001 PHE A 33 TYR 0.011 0.001 TYR A 69 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 86 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6174 (ttp) cc_final: 0.5592 (tmm) REVERT: A 103 ARG cc_start: 0.7444 (mpt180) cc_final: 0.6877 (mmt-90) REVERT: A 117 SER cc_start: 0.9159 (t) cc_final: 0.8921 (t) REVERT: C 13 MET cc_start: 0.6545 (tmm) cc_final: 0.6200 (ptm) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.2094 time to fit residues: 18.7920 Evaluate side-chains 78 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3478 Z= 0.144 Angle : 0.488 6.705 4772 Z= 0.249 Chirality : 0.047 0.134 554 Planarity : 0.005 0.041 605 Dihedral : 3.670 22.445 498 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.63 % Allowed : 9.57 % Favored : 86.80 % 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: 0.81 (0.41), residues: 459 helix: -1.39 (0.75), residues: 34 sheet: 1.36 (0.38), residues: 223 loop : 0.00 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.001 0.000 HIS C 88 PHE 0.008 0.001 PHE D 33 TYR 0.008 0.001 TYR A 69 ARG 0.006 0.000 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 86 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.6156 (ttp) cc_final: 0.5644 (tmm) REVERT: A 117 SER cc_start: 0.9193 (t) cc_final: 0.8967 (t) REVERT: B 54 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: C 13 MET cc_start: 0.6541 (tmm) cc_final: 0.6161 (ptm) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.2233 time to fit residues: 20.3715 Evaluate side-chains 77 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 54 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3478 Z= 0.168 Angle : 0.495 6.637 4772 Z= 0.253 Chirality : 0.047 0.134 554 Planarity : 0.005 0.038 605 Dihedral : 3.660 22.371 498 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.63 % Allowed : 10.23 % Favored : 86.14 % 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: 0.74 (0.41), residues: 459 helix: -1.42 (0.76), residues: 34 sheet: 1.29 (0.38), residues: 223 loop : -0.00 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.001 0.001 HIS C 88 PHE 0.007 0.001 PHE D 33 TYR 0.015 0.001 TYR C 78 ARG 0.006 0.000 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 80 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.6198 (ttp) cc_final: 0.5669 (tmm) REVERT: A 117 SER cc_start: 0.9188 (t) cc_final: 0.8964 (t) REVERT: C 13 MET cc_start: 0.6557 (tmm) cc_final: 0.6142 (ptm) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2137 time to fit residues: 17.9842 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 75 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.1432 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= 0.266 Angle : 0.541 6.491 4772 Z= 0.280 Chirality : 0.049 0.137 554 Planarity : 0.005 0.042 605 Dihedral : 4.019 22.115 498 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.29 % Allowed : 11.55 % 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: 0.53 (0.41), residues: 459 helix: -1.21 (0.84), residues: 34 sheet: 1.02 (0.38), residues: 223 loop : -0.04 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.002 0.001 HIS C 88 PHE 0.011 0.001 PHE D 33 TYR 0.015 0.001 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 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.343 Fit side-chains REVERT: A 13 MET cc_start: 0.6314 (ttp) cc_final: 0.5745 (tmm) REVERT: A 103 ARG cc_start: 0.7470 (mpt180) cc_final: 0.6982 (mmt-90) REVERT: A 117 SER cc_start: 0.9201 (t) cc_final: 0.8991 (t) REVERT: C 13 MET cc_start: 0.6470 (tmm) cc_final: 0.6122 (ptm) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.2198 time to fit residues: 16.8688 Evaluate side-chains 71 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 60 THR Chi-restraints excluded: chain B residue 75 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3478 Z= 0.306 Angle : 0.562 6.528 4772 Z= 0.293 Chirality : 0.049 0.139 554 Planarity : 0.005 0.036 605 Dihedral : 4.243 22.734 498 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.29 % Allowed : 13.20 % Favored : 82.51 % 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: -0.41 (1.00), residues: 28 sheet: 0.75 (0.38), residues: 223 loop : -0.19 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 PHE 0.012 0.002 PHE D 33 TYR 0.013 0.002 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 78 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7482 (mpt180) cc_final: 0.6982 (mmt-90) REVERT: A 117 SER cc_start: 0.9203 (t) cc_final: 0.8998 (t) REVERT: C 13 MET cc_start: 0.6485 (tmm) cc_final: 0.6152 (ptm) REVERT: C 15 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7770 (tmtt) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.2099 time to fit residues: 16.4557 Evaluate side-chains 77 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 60 THR Chi-restraints excluded: chain B residue 75 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 C residue 96 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3478 Z= 0.175 Angle : 0.500 6.611 4772 Z= 0.256 Chirality : 0.047 0.134 554 Planarity : 0.005 0.043 605 Dihedral : 3.892 23.838 498 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.63 % Allowed : 13.53 % 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: 0.41 (0.41), residues: 459 helix: -0.44 (0.97), residues: 28 sheet: 0.87 (0.39), residues: 223 loop : -0.21 (0.41), residues: 208 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 0.007 0.001 PHE D 87 TYR 0.014 0.001 TYR C 105 ARG 0.006 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 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7427 (mpt180) cc_final: 0.6970 (mmt-90) REVERT: A 117 SER cc_start: 0.9186 (t) cc_final: 0.8972 (t) REVERT: C 13 MET cc_start: 0.6534 (tmm) cc_final: 0.6180 (ptm) REVERT: C 15 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7639 (tmtt) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.2132 time to fit residues: 16.9677 Evaluate side-chains 75 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 75 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 C residue 96 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3478 Z= 0.195 Angle : 0.507 6.551 4772 Z= 0.261 Chirality : 0.048 0.134 554 Planarity : 0.005 0.044 605 Dihedral : 3.880 23.431 498 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.96 % Allowed : 14.19 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.41), residues: 459 helix: -1.14 (0.86), residues: 34 sheet: 0.87 (0.39), residues: 223 loop : -0.26 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.002 0.001 HIS B 88 PHE 0.008 0.001 PHE D 33 TYR 0.013 0.001 TYR C 105 ARG 0.007 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 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 SER cc_start: 0.9190 (t) cc_final: 0.8973 (t) REVERT: C 13 MET cc_start: 0.6532 (tmm) cc_final: 0.6207 (ttp) REVERT: C 15 LYS cc_start: 0.8106 (tmtt) cc_final: 0.7614 (tmtt) REVERT: C 35 LYS cc_start: 0.7658 (tptp) cc_final: 0.7446 (tptp) outliers start: 12 outliers final: 12 residues processed: 71 average time/residue: 0.2220 time to fit residues: 18.3269 Evaluate side-chains 77 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 75 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 C residue 96 THR Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 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 27 ASN D 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1833 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= 0.161 Angle : 0.494 6.573 4772 Z= 0.254 Chirality : 0.047 0.132 554 Planarity : 0.005 0.047 605 Dihedral : 3.777 23.713 498 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.63 % Allowed : 14.52 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.41), residues: 459 helix: -1.16 (0.86), residues: 33 sheet: 0.92 (0.39), residues: 223 loop : -0.29 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.002 0.000 HIS B 88 PHE 0.007 0.001 PHE D 87 TYR 0.012 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 78 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 SER cc_start: 0.9162 (t) cc_final: 0.8944 (t) REVERT: C 13 MET cc_start: 0.6560 (tmm) cc_final: 0.6127 (ptm) REVERT: C 15 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7594 (tmtt) REVERT: C 35 LYS cc_start: 0.7674 (tptp) cc_final: 0.7463 (tptp) REVERT: C 78 TYR cc_start: 0.7139 (t80) cc_final: 0.6813 (m-80) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.2294 time to fit residues: 18.9938 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 75 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 C residue 96 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 D 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1976 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= 0.153 Angle : 0.496 6.619 4772 Z= 0.253 Chirality : 0.047 0.132 554 Planarity : 0.005 0.049 605 Dihedral : 3.695 23.620 498 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.63 % Allowed : 16.17 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.41), residues: 459 helix: -1.22 (0.84), residues: 33 sheet: 0.99 (0.39), residues: 223 loop : -0.29 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.001 0.000 HIS B 88 PHE 0.006 0.001 PHE D 87 TYR 0.016 0.001 TYR C 105 ARG 0.007 0.001 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 80 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 SER cc_start: 0.9160 (t) cc_final: 0.8936 (t) REVERT: C 15 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7662 (tmtt) REVERT: C 35 LYS cc_start: 0.7681 (tptp) cc_final: 0.7471 (tptp) REVERT: C 78 TYR cc_start: 0.7137 (t80) cc_final: 0.6854 (m-80) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.2181 time to fit residues: 18.6476 Evaluate side-chains 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 60 THR Chi-restraints excluded: chain B residue 75 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 C residue 96 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.0970 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126999 restraints weight = 4648.651| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.54 r_work: 0.3535 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2148 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= 0.124 Angle : 0.481 6.571 4772 Z= 0.243 Chirality : 0.047 0.129 554 Planarity : 0.005 0.051 605 Dihedral : 3.528 23.995 498 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.64 % Allowed : 18.15 % Favored : 79.21 % 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: 0.47 (0.41), residues: 459 helix: -1.33 (0.81), residues: 33 sheet: 1.12 (0.39), residues: 223 loop : -0.26 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.001 0.000 HIS B 88 PHE 0.007 0.001 PHE D 87 TYR 0.012 0.001 TYR C 105 ARG 0.007 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.35 seconds wall clock time: 23 minutes 34.85 seconds (1414.85 seconds total)