Starting phenix.real_space_refine on Mon Mar 11 06:21:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a93_15267/03_2024/8a93_15267_updated.pdb" } resolution = 3.05 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 7 5.16 5 C 4491 2.51 5 N 1388 2.21 5 O 1417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 246": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7353 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2692 Chain: "B" Number of atoms: 2643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2673 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 81 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 323 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 685 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "X" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.39, per 1000 atoms: 1.55 Number of scatterers: 7353 At special positions: 0 Unit cell: (82.56, 99.76, 111.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 7 16.00 P 48 15.00 Mg 2 11.99 O 1417 8.00 N 1388 7.00 C 4491 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: 3.40 Conformation dependent library (CDL) restraints added in 2.2 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 9 sheets defined 45.9% alpha, 14.0% beta 11 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.680A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 162 Processing helix chain 'A' and resid 169 through 203 removed outlier: 3.896A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 3.943A pdb=" N ALA A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 262 through 284 Processing helix chain 'A' and resid 301 through 313 removed outlier: 4.292A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.955A pdb=" N GLU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.762A pdb=" N LEU B 118 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 119 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 142 through 162 Processing helix chain 'B' and resid 170 through 204 removed outlier: 4.061A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.692A pdb=" N SER B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 256 through 259 No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 262 through 284 Processing helix chain 'B' and resid 301 through 313 removed outlier: 4.161A pdb=" N ALA B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 removed outlier: 3.636A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 16 removed outlier: 3.568A pdb=" N ARG D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.656A pdb=" N GLN D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.713A pdb=" N ALA D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 95 removed outlier: 3.772A pdb=" N SER F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 removed outlier: 3.863A pdb=" N ARG F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 159 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 29 removed outlier: 6.987A pdb=" N ALA A 317 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 28 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 319 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 290 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA A 320 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 292 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 86 removed outlier: 6.667A pdb=" N GLU A 73 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU A 3 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.613A pdb=" N ASP A 246 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 332 through 334 Processing sheet with id= E, first strand: chain 'B' and resid 24 through 29 removed outlier: 3.702A pdb=" N ALA B 317 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU B 290 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ALA B 320 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL B 292 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 85 removed outlier: 7.013A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.533A pdb=" N ASP B 246 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 331 through 334 Processing sheet with id= I, first strand: chain 'F' and resid 101 through 104 297 hydrogen bonds defined for protein. 842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2126 1.33 - 1.45: 1259 1.45 - 1.57: 4084 1.57 - 1.69: 94 1.69 - 1.81: 10 Bond restraints: 7573 Sorted by residual: bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.593 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 7568 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.13: 508 107.13 - 113.94: 4224 113.94 - 120.74: 3319 120.74 - 127.54: 2268 127.54 - 134.34: 127 Bond angle restraints: 10446 Sorted by residual: angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O3A ANP A 901 " ideal model delta sigma weight residual 103.40 114.41 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O3A ANP B 901 " ideal model delta sigma weight residual 103.40 114.37 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" PA ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 125.41 133.35 -7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" PA ANP B 901 " pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 125.41 133.13 -7.72 3.00e+00 1.11e-01 6.61e+00 angle pdb=" CB LYS F 118 " pdb=" CG LYS F 118 " pdb=" CD LYS F 118 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.53e+00 ... (remaining 10441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3752 17.95 - 35.89: 460 35.89 - 53.84: 237 53.84 - 71.79: 29 71.79 - 89.73: 10 Dihedral angle restraints: 4488 sinusoidal: 2139 harmonic: 2349 Sorted by residual: dihedral pdb=" CG ARG B 191 " pdb=" CD ARG B 191 " pdb=" NE ARG B 191 " pdb=" CZ ARG B 191 " ideal model delta sinusoidal sigma weight residual 90.00 134.98 -44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CB GLU A 17 " pdb=" CG GLU A 17 " pdb=" CD GLU A 17 " pdb=" OE1 GLU A 17 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA GLU B 294 " pdb=" C GLU B 294 " pdb=" N TRP B 295 " pdb=" CA TRP B 295 " ideal model delta harmonic sigma weight residual 180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1056 0.057 - 0.113: 112 0.113 - 0.170: 4 0.170 - 0.227: 0 0.227 - 0.283: 2 Chirality restraints: 1174 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL F 161 " pdb=" N VAL F 161 " pdb=" C VAL F 161 " pdb=" CB VAL F 161 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1171 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 114 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 115 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 123 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 124 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 58 2.64 - 3.20: 5888 3.20 - 3.77: 10431 3.77 - 4.33: 14010 4.33 - 4.90: 23018 Nonbonded interactions: 53405 Sorted by model distance: nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.078 2.170 nonbonded pdb=" O1B ANP B 901 " pdb="MG MG B 902 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.145 2.170 ... (remaining 53400 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 1 through 51 or resid 53 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ gh 341 or resid 901 through 902)) selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 341 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.200 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: 16.700 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 0.166 7573 Z= 0.248 Angle : 0.574 11.006 10446 Z= 0.271 Chirality : 0.036 0.283 1174 Planarity : 0.004 0.035 1203 Dihedral : 18.984 89.732 2982 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.64 % Allowed : 0.00 % Favored : 99.36 % 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: 1.45 (0.31), residues: 818 helix: 2.68 (0.28), residues: 355 sheet: 0.94 (0.42), residues: 148 loop : -1.14 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 PHE 0.008 0.001 PHE D 34 TYR 0.004 0.001 TYR B 178 ARG 0.008 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: D 16 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7720 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3073 time to fit residues: 33.0578 Evaluate side-chains 71 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 7573 Z= 0.313 Angle : 0.589 5.553 10446 Z= 0.307 Chirality : 0.039 0.151 1174 Planarity : 0.004 0.032 1203 Dihedral : 19.815 89.619 1458 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.44 % Allowed : 6.70 % Favored : 91.87 % 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: 1.17 (0.30), residues: 818 helix: 2.43 (0.28), residues: 363 sheet: 1.20 (0.41), residues: 143 loop : -1.57 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.007 0.001 HIS A 277 PHE 0.013 0.001 PHE A 193 TYR 0.009 0.001 TYR F 102 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.778 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.3108 time to fit residues: 29.9573 Evaluate side-chains 67 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.0070 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7573 Z= 0.153 Angle : 0.483 5.175 10446 Z= 0.252 Chirality : 0.035 0.141 1174 Planarity : 0.004 0.037 1203 Dihedral : 19.316 86.315 1458 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.12 % Allowed : 8.77 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 818 helix: 2.47 (0.28), residues: 366 sheet: 1.28 (0.41), residues: 148 loop : -1.38 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 67 HIS 0.003 0.001 HIS A 257 PHE 0.009 0.001 PHE D 34 TYR 0.011 0.001 TYR F 102 ARG 0.004 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.814 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.3108 time to fit residues: 29.5341 Evaluate side-chains 74 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7573 Z= 0.269 Angle : 0.525 5.412 10446 Z= 0.273 Chirality : 0.037 0.139 1174 Planarity : 0.004 0.036 1203 Dihedral : 19.245 87.729 1458 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 10.85 % Favored : 87.72 % 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: 1.25 (0.30), residues: 818 helix: 2.43 (0.28), residues: 363 sheet: 1.49 (0.41), residues: 143 loop : -1.57 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 105 HIS 0.007 0.001 HIS A 277 PHE 0.012 0.001 PHE A 193 TYR 0.016 0.001 TYR F 102 ARG 0.003 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.796 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.3152 time to fit residues: 28.6413 Evaluate side-chains 69 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 7573 Z= 0.469 Angle : 0.653 6.852 10446 Z= 0.338 Chirality : 0.042 0.144 1174 Planarity : 0.005 0.043 1203 Dihedral : 19.429 88.968 1458 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.23 % Allowed : 12.12 % Favored : 85.65 % 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: 0.71 (0.29), residues: 818 helix: 2.12 (0.28), residues: 360 sheet: 1.06 (0.42), residues: 143 loop : -1.91 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.009 0.002 HIS A 277 PHE 0.019 0.002 PHE A 193 TYR 0.009 0.002 TYR B 79 ARG 0.005 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.799 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.2941 time to fit residues: 27.8037 Evaluate side-chains 68 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 80 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7573 Z= 0.161 Angle : 0.511 9.263 10446 Z= 0.264 Chirality : 0.036 0.161 1174 Planarity : 0.004 0.038 1203 Dihedral : 19.230 89.816 1458 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.28 % Allowed : 12.92 % Favored : 85.81 % 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: 1.20 (0.30), residues: 818 helix: 2.52 (0.28), residues: 359 sheet: 1.34 (0.40), residues: 143 loop : -1.64 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.003 0.001 HIS A 257 PHE 0.010 0.001 PHE D 34 TYR 0.007 0.001 TYR B 178 ARG 0.003 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.3189 time to fit residues: 29.5812 Evaluate side-chains 67 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7573 Z= 0.220 Angle : 0.514 8.153 10446 Z= 0.266 Chirality : 0.036 0.160 1174 Planarity : 0.004 0.034 1203 Dihedral : 19.249 89.681 1458 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.44 % Allowed : 12.76 % Favored : 85.81 % 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: 1.25 (0.30), residues: 818 helix: 2.49 (0.28), residues: 360 sheet: 1.43 (0.40), residues: 143 loop : -1.57 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 PHE 0.010 0.001 PHE A 193 TYR 0.013 0.001 TYR F 102 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.819 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.3082 time to fit residues: 26.6788 Evaluate side-chains 67 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7573 Z= 0.153 Angle : 0.487 8.032 10446 Z= 0.250 Chirality : 0.035 0.163 1174 Planarity : 0.004 0.034 1203 Dihedral : 19.120 85.212 1458 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.28 % Allowed : 13.08 % Favored : 85.65 % 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: 1.46 (0.31), residues: 818 helix: 2.62 (0.28), residues: 361 sheet: 1.40 (0.41), residues: 148 loop : -1.40 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 257 PHE 0.008 0.001 PHE D 34 TYR 0.006 0.001 TYR B 178 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.798 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.2893 time to fit residues: 27.3666 Evaluate side-chains 72 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain F residue 139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7573 Z= 0.263 Angle : 0.538 7.569 10446 Z= 0.276 Chirality : 0.037 0.159 1174 Planarity : 0.004 0.033 1203 Dihedral : 19.212 86.961 1458 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.44 % Allowed : 12.76 % Favored : 85.81 % 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: 1.29 (0.30), residues: 818 helix: 2.49 (0.28), residues: 361 sheet: 1.48 (0.40), residues: 143 loop : -1.55 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 105 HIS 0.006 0.001 HIS A 277 PHE 0.012 0.001 PHE A 193 TYR 0.016 0.001 TYR F 102 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.707 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.3058 time to fit residues: 26.3637 Evaluate side-chains 70 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7573 Z= 0.211 Angle : 0.519 7.481 10446 Z= 0.266 Chirality : 0.036 0.160 1174 Planarity : 0.004 0.032 1203 Dihedral : 19.186 86.483 1458 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.44 % Allowed : 12.92 % Favored : 85.65 % 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: 1.30 (0.30), residues: 818 helix: 2.51 (0.28), residues: 361 sheet: 1.30 (0.40), residues: 148 loop : -1.49 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.005 0.001 HIS A 277 PHE 0.009 0.001 PHE A 193 TYR 0.006 0.001 TYR B 79 ARG 0.003 0.000 ARG A 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.790 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.3112 time to fit residues: 27.8710 Evaluate side-chains 71 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.075280 restraints weight = 30226.630| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.58 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7573 Z= 0.149 Angle : 0.488 7.344 10446 Z= 0.248 Chirality : 0.035 0.161 1174 Planarity : 0.004 0.034 1203 Dihedral : 19.055 82.277 1458 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.44 % Allowed : 12.76 % Favored : 85.81 % 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: 1.52 (0.31), residues: 818 helix: 2.59 (0.28), residues: 362 sheet: 1.37 (0.41), residues: 153 loop : -1.28 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 67 HIS 0.003 0.001 HIS A 257 PHE 0.009 0.001 PHE D 34 TYR 0.019 0.001 TYR F 102 ARG 0.003 0.000 ARG A 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.86 seconds wall clock time: 32 minutes 41.52 seconds (1961.52 seconds total)