Starting phenix.real_space_refine on Mon Jun 24 16:59:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/06_2024/8ve0_43160_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2281 2.51 5 N 588 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" 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: 3527 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 875 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 878 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 867 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.90, per 1000 atoms: 0.82 Number of scatterers: 3527 At special positions: 0 Unit cell: (77.556, 68.002, 61.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 651 8.00 N 588 7.00 C 2281 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 655.3 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 8 sheets defined 6.7% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'D' and resid 75 through 82 removed outlier: 3.689A 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: 6.993A pdb=" N TYR A 105 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LYS A 15 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 107 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU A 17 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA A 109 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 97 removed outlier: 3.730A pdb=" N GLY A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.404A 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: 7.143A pdb=" N TYR B 105 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LYS B 15 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 107 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 17 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.713A 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: 3.631A pdb=" N GLY B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.506A 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: 6.877A pdb=" N TYR C 105 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LYS C 15 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 107 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU C 17 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 109 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 90 through 97 removed outlier: 5.207A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 29 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.657A 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: 6.695A pdb=" N TYR D 105 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LYS D 15 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE D 107 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU D 17 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA D 109 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 91 through 97 removed outlier: 5.105A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 318 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: 0.84 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 559 1.31 - 1.44: 1036 1.44 - 1.56: 2017 1.56 - 1.68: 2 1.68 - 1.81: 10 Bond restraints: 3624 Sorted by residual: bond pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 1.461 1.570 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" CAH 1WZ B 201 " pdb=" CAR 1WZ B 201 " ideal model delta sigma weight residual 1.461 1.569 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" CAV 1WZ B 201 " pdb=" NAW 1WZ B 201 " ideal model delta sigma weight residual 1.376 1.473 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CAV 1WZ C 201 " pdb=" NAW 1WZ C 201 " ideal model delta sigma weight residual 1.376 1.472 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 1.464 1.548 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 3619 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.42: 157 107.42 - 114.06: 2053 114.06 - 120.70: 1435 120.70 - 127.34: 1256 127.34 - 133.98: 56 Bond angle restraints: 4957 Sorted by residual: angle pdb=" CAH 1WZ B 201 " pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 126.24 115.98 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CAH 1WZ C 201 " pdb=" CAI 1WZ C 201 " pdb=" CAS 1WZ C 201 " ideal model delta sigma weight residual 126.24 116.06 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 108.33 5.77 2.00e+00 2.50e-01 8.32e+00 angle pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " pdb=" CD LYS C 80 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 110.29 113.46 -3.17 1.28e+00 6.10e-01 6.12e+00 ... (remaining 4952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1914 16.46 - 32.92: 135 32.92 - 49.38: 32 49.38 - 65.84: 8 65.84 - 82.30: 6 Dihedral angle restraints: 2095 sinusoidal: 737 harmonic: 1358 Sorted by residual: dihedral pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " ideal model delta sinusoidal sigma weight residual -180.00 -126.43 -53.57 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS C 15 " pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sinusoidal sigma weight residual -180.00 -129.56 -50.44 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " pdb=" CE LYS B 15 " ideal model delta sinusoidal sigma weight residual 60.00 10.16 49.84 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 2092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 331 0.026 - 0.052: 126 0.052 - 0.078: 39 0.078 - 0.104: 32 0.104 - 0.130: 37 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 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 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 4.04e-01 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 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 562 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 113 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO B 113 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 23 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 24 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.015 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 556 2.77 - 3.30: 3079 3.30 - 3.83: 5897 3.83 - 4.37: 6636 4.37 - 4.90: 12429 Nonbonded interactions: 28597 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 77 " model vdw 2.234 2.440 nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.238 2.440 nonbonded pdb=" OD2 ASP D 18 " pdb=" OH TYR D 78 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 117 " pdb=" OAG 1WZ C 201 " model vdw 2.310 2.440 nonbonded pdb=" OE2 GLU C 89 " pdb=" OG1 THR D 96 " model vdw 2.329 2.440 ... (remaining 28592 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 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 62 or (resid 63 and ( \ name N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 thr \ ough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 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 91 or (resid 92 and (name N or name CA or name C or name O or \ name CB )) or resid 93 through 95 or (resid 96 through 97 and (name N or name CA \ or name C or name O or name CB )) or resid 98 through 103 or (resid 104 and (na \ me N or name CA or name C or name O or name CB )) or resid 105 through 122 or (r \ esid 123 and (name N or name CA or name C or name O or name CB )) or resid 124)) \ selection = (chain 'B' and (resid 10 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 37 or (resid 38 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 or (res \ id 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 50 or (resid 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 58 or (resid 59 through 63 and (name N or name CA o \ r 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 76 or (resid 7 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 78 through 9 \ 8 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 name C or n \ ame O or name CB )) or resid 105 through 122 or (resid 123 and (name N or name C \ A or name C or name O or name CB )) or resid 124)) 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 through 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 58 or (resid 59 through 63 and (name N or name CA or name C or n \ ame O or name CB )) or resid 64 through 91 or (resid 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 95 or (resid 96 through 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 or (resid 9 \ 9 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 name C or name O or name \ CB )) or resid 105 through 122 or (resid 123 and (name N or name CA or name C o \ r name O or name CB )) or resid 124)) selection = (chain 'D' 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 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 50 or (resid 51 and (name N or name CA or name C or \ name O or name CB )) or resid 52 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 65 or (resid 6 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 67 through 7 \ 6 or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 95 or (resid 96 through 97 and (name N or name CA or name C or name \ O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA or n \ ame C or name O or name CB )) or resid 101 through 124)) } 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: 0.700 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: 3.330 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 3624 Z= 0.391 Angle : 0.621 10.259 4957 Z= 0.318 Chirality : 0.045 0.130 565 Planarity : 0.004 0.040 627 Dihedral : 13.407 82.301 1219 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.57 % Allowed : 0.00 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.38), residues: 458 helix: 0.66 (0.86), residues: 34 sheet: 2.28 (0.33), residues: 240 loop : -0.36 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS D 90 PHE 0.009 0.001 PHE A 64 TYR 0.017 0.001 TYR B 78 ARG 0.004 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.390 Fit side-chains REVERT: C 44 PHE cc_start: 0.8001 (t80) cc_final: 0.7721 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1723 time to fit residues: 19.3947 Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.0020 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3624 Z= 0.176 Angle : 0.498 3.839 4957 Z= 0.259 Chirality : 0.047 0.137 565 Planarity : 0.004 0.029 627 Dihedral : 6.167 70.900 503 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.14 % Allowed : 9.40 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.38), residues: 458 helix: 1.51 (0.93), residues: 34 sheet: 2.51 (0.34), residues: 212 loop : -0.56 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 PHE 0.010 0.001 PHE B 33 TYR 0.010 0.001 TYR D 116 ARG 0.003 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.370 Fit side-chains REVERT: C 44 PHE cc_start: 0.7940 (t80) cc_final: 0.7686 (t80) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.1853 time to fit residues: 18.3558 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3624 Z= 0.151 Angle : 0.460 3.611 4957 Z= 0.240 Chirality : 0.046 0.133 565 Planarity : 0.004 0.026 627 Dihedral : 5.506 66.784 503 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.71 % Allowed : 13.11 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.38), residues: 458 helix: 1.34 (0.89), residues: 36 sheet: 2.56 (0.35), residues: 212 loop : -0.67 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.002 0.001 HIS C 56 PHE 0.008 0.001 PHE A 33 TYR 0.010 0.001 TYR B 116 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.389 Fit side-chains REVERT: C 44 PHE cc_start: 0.7958 (t80) cc_final: 0.7666 (t80) outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.1717 time to fit residues: 16.1830 Evaluate side-chains 76 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3624 Z= 0.146 Angle : 0.456 4.038 4957 Z= 0.236 Chirality : 0.046 0.132 565 Planarity : 0.004 0.028 627 Dihedral : 5.243 64.198 503 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 458 helix: 1.50 (0.90), residues: 36 sheet: 2.58 (0.35), residues: 210 loop : -0.70 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS D 88 PHE 0.008 0.001 PHE A 33 TYR 0.010 0.001 TYR D 116 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.356 Fit side-chains REVERT: C 44 PHE cc_start: 0.7952 (t80) cc_final: 0.7676 (t80) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.1888 time to fit residues: 16.4917 Evaluate side-chains 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3624 Z= 0.236 Angle : 0.511 4.384 4957 Z= 0.265 Chirality : 0.048 0.136 565 Planarity : 0.004 0.035 627 Dihedral : 5.526 60.530 503 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 16.81 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.39), residues: 458 helix: 1.37 (0.89), residues: 36 sheet: 2.34 (0.35), residues: 210 loop : -0.73 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.003 0.001 HIS B 88 PHE 0.013 0.002 PHE B 33 TYR 0.011 0.001 TYR B 116 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.400 Fit side-chains REVERT: C 44 PHE cc_start: 0.7974 (t80) cc_final: 0.7698 (t80) REVERT: D 84 ILE cc_start: 0.8086 (mt) cc_final: 0.7881 (mt) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1893 time to fit residues: 18.3732 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3624 Z= 0.369 Angle : 0.597 5.869 4957 Z= 0.309 Chirality : 0.050 0.141 565 Planarity : 0.005 0.047 627 Dihedral : 5.989 66.106 503 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.42 % Allowed : 17.38 % Favored : 79.20 % 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: 0.92 (0.39), residues: 458 helix: 1.37 (0.90), residues: 34 sheet: 1.97 (0.36), residues: 209 loop : -1.01 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 79 HIS 0.004 0.001 HIS B 31 PHE 0.016 0.002 PHE B 33 TYR 0.012 0.002 TYR B 116 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.390 Fit side-chains REVERT: B 17 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7960 (mt) REVERT: C 44 PHE cc_start: 0.8022 (t80) cc_final: 0.7679 (t80) REVERT: D 84 ILE cc_start: 0.8163 (mt) cc_final: 0.7943 (mt) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.1784 time to fit residues: 18.4281 Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR 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: 7.9990 chunk 23 optimal weight: 0.0010 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3624 Z= 0.172 Angle : 0.498 5.612 4957 Z= 0.257 Chirality : 0.047 0.136 565 Planarity : 0.004 0.046 627 Dihedral : 5.341 54.888 503 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.13 % Allowed : 19.09 % Favored : 77.78 % 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: 1.09 (0.39), residues: 458 helix: 1.36 (0.90), residues: 34 sheet: 2.09 (0.35), residues: 210 loop : -0.90 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.001 0.001 HIS A 88 PHE 0.010 0.001 PHE A 33 TYR 0.009 0.001 TYR D 116 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.426 Fit side-chains REVERT: C 44 PHE cc_start: 0.7992 (t80) cc_final: 0.7644 (t80) REVERT: D 84 ILE cc_start: 0.8118 (mt) cc_final: 0.7908 (mt) REVERT: D 89 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6766 (mt-10) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.1888 time to fit residues: 18.7746 Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.0670 overall best weight: 2.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3624 Z= 0.252 Angle : 0.549 6.182 4957 Z= 0.282 Chirality : 0.049 0.137 565 Planarity : 0.004 0.049 627 Dihedral : 5.529 58.723 503 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.70 % Allowed : 17.95 % Favored : 78.35 % 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: 0.95 (0.39), residues: 458 helix: 1.12 (0.89), residues: 36 sheet: 1.97 (0.35), residues: 210 loop : -0.95 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A 88 PHE 0.012 0.002 PHE B 33 TYR 0.011 0.001 TYR B 116 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.412 Fit side-chains REVERT: A 34 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7207 (ttt-90) REVERT: B 17 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 44 PHE cc_start: 0.8015 (t80) cc_final: 0.7655 (t80) REVERT: D 89 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6521 (mt-10) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.1882 time to fit residues: 19.1813 Evaluate side-chains 89 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3624 Z= 0.133 Angle : 0.486 6.678 4957 Z= 0.249 Chirality : 0.047 0.135 565 Planarity : 0.004 0.039 627 Dihedral : 4.916 46.355 503 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.71 % Allowed : 20.80 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.39), residues: 458 helix: 1.41 (0.94), residues: 34 sheet: 2.20 (0.35), residues: 210 loop : -0.82 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.001 0.000 HIS C 88 PHE 0.007 0.001 PHE A 33 TYR 0.010 0.001 TYR D 116 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.379 Fit side-chains REVERT: C 42 GLU cc_start: 0.7894 (pt0) cc_final: 0.7444 (pt0) REVERT: C 44 PHE cc_start: 0.7998 (t80) cc_final: 0.7706 (t80) REVERT: D 89 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6731 (mt-10) outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.1877 time to fit residues: 18.2125 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3624 Z= 0.184 Angle : 0.520 7.059 4957 Z= 0.267 Chirality : 0.047 0.134 565 Planarity : 0.004 0.036 627 Dihedral : 5.051 50.101 503 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.28 % Allowed : 19.94 % Favored : 77.78 % 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: 1.24 (0.39), residues: 458 helix: 1.33 (0.94), residues: 36 sheet: 2.15 (0.35), residues: 211 loop : -0.75 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 PHE 0.009 0.001 PHE B 33 TYR 0.011 0.001 TYR D 116 ARG 0.003 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.372 Fit side-chains REVERT: A 34 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7215 (ttt-90) REVERT: C 44 PHE cc_start: 0.8016 (t80) cc_final: 0.7708 (t80) REVERT: D 89 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6832 (mt-10) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.1730 time to fit residues: 16.6099 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 17 optimal weight: 7.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133130 restraints weight = 4868.837| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.51 r_work: 0.3600 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3624 Z= 0.147 Angle : 0.493 7.032 4957 Z= 0.254 Chirality : 0.047 0.131 565 Planarity : 0.004 0.028 627 Dihedral : 4.860 46.182 503 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 19.66 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.39), residues: 458 helix: 1.29 (0.93), residues: 36 sheet: 2.25 (0.35), residues: 210 loop : -0.73 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS A 88 PHE 0.007 0.001 PHE A 33 TYR 0.010 0.001 TYR D 116 ARG 0.003 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.22 seconds wall clock time: 23 minutes 2.80 seconds (1382.80 seconds total)