Starting phenix.real_space_refine on Fri Dec 8 08:18:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/12_2023/8bmq_16121_updated.pdb" } resolution = 3.6 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= 0.010 sd= 0.098 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 6 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5044 2.51 5 N 1283 2.21 5 O 1414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2137 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2162 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2101 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 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: 4.60, per 1000 atoms: 0.59 Number of scatterers: 7784 At special positions: 0 Unit cell: (79.716, 83.804, 128.772, 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 36 16.00 P 6 15.00 Mg 1 11.99 O 1414 8.00 N 1283 7.00 C 5044 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 53.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.215A pdb=" N GLU A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.747A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.904A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.763A pdb=" N GLY A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.564A pdb=" N HIS B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.119A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.959A pdb=" N PHE B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.798A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.931A pdb=" N ALA B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.616A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 Processing helix chain 'C' and resid 13 through 30 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 74 removed outlier: 4.406A pdb=" N ALA C 62 " --> pdb=" O TRP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 100 removed outlier: 3.825A pdb=" N GLY C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'C' and resid 146 through 171 Proline residue: C 153 - end of helix removed outlier: 4.720A pdb=" N VAL C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 18 Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.923A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 62 through 86 Proline residue: D 71 - end of helix removed outlier: 5.019A pdb=" N TRP D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N MET D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 128 removed outlier: 3.793A pdb=" N ARG D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 removed outlier: 4.174A pdb=" N THR D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix removed outlier: 4.697A pdb=" N LEU D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 192 through 225 removed outlier: 4.338A pdb=" N VAL D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Proline residue: D 202 - end of helix Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 244 through 261 Proline residue: D 248 - end of helix removed outlier: 3.705A pdb=" N LEU D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU D 255 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.709A pdb=" N ILE A 30 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE A 5 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 28 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 212 through 216 Processing sheet with id= C, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.704A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.432A pdb=" N ASP B 214 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 39 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 216 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 225 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.021A pdb=" N THR B 197 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 169 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 199 " --> pdb=" O LEU B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 33 through 35 347 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2451 1.34 - 1.46: 1198 1.46 - 1.57: 4220 1.57 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 7949 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP B 301 " pdb=" PB ANP B 301 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O5' ANP A 301 " pdb=" PA ANP A 301 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 7944 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.79: 139 104.79 - 112.14: 4068 112.14 - 119.49: 2722 119.49 - 126.84: 3724 126.84 - 134.19: 128 Bond angle restraints: 10781 Sorted by residual: angle pdb=" PB ANP A 301 " pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP B 301 " pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 126.95 107.82 19.13 3.00e+00 1.11e-01 4.06e+01 angle pdb=" O1B ANP B 301 " pdb=" PB ANP B 301 " pdb=" O2B ANP B 301 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C LEU A 174 " pdb=" N ASP A 175 " pdb=" CA ASP A 175 " ideal model delta sigma weight residual 120.65 125.64 -4.99 1.36e+00 5.41e-01 1.35e+01 angle pdb=" O1B ANP A 301 " pdb=" PB ANP A 301 " pdb=" O2B ANP A 301 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 10776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4255 17.69 - 35.39: 383 35.39 - 53.08: 72 53.08 - 70.78: 31 70.78 - 88.47: 14 Dihedral angle restraints: 4755 sinusoidal: 1931 harmonic: 2824 Sorted by residual: dihedral pdb=" CA SER A 103 " pdb=" C SER A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " pdb=" OD1 ASP A 211 " ideal model delta sinusoidal sigma weight residual -30.00 -85.09 55.09 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA THR B 197 " pdb=" C THR B 197 " pdb=" N VAL B 198 " pdb=" CA VAL B 198 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1027 0.056 - 0.113: 190 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C3' ANP B 301 " pdb=" C2' ANP B 301 " pdb=" C4' ANP B 301 " pdb=" O3' ANP B 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' ANP A 301 " pdb=" C2' ANP A 301 " pdb=" C4' ANP A 301 " pdb=" O3' ANP A 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1240 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 47 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C GLY C 47 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY C 47 " 0.011 2.00e-02 2.50e+03 pdb=" N SER C 48 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 93 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 198 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL B 198 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 198 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 199 " -0.009 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 7998 3.27 - 3.82: 12381 3.82 - 4.36: 14434 4.36 - 4.90: 25483 Nonbonded interactions: 60850 Sorted by model distance: nonbonded pdb=" O1B ANP B 301 " pdb=" O2G ANP B 301 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASN D 40 " pdb=" N TRP D 41 " model vdw 2.203 2.520 nonbonded pdb=" OD1 ASP B 170 " pdb="MG MG B 302 " model vdw 2.251 2.170 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.253 2.440 ... (remaining 60845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.040 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 0.146 7949 Z= 0.425 Angle : 0.756 19.200 10781 Z= 0.355 Chirality : 0.046 0.282 1243 Planarity : 0.004 0.041 1336 Dihedral : 15.483 88.472 2935 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 975 helix: 0.76 (0.23), residues: 547 sheet: -0.74 (0.60), residues: 70 loop : -1.07 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 58 HIS 0.005 0.001 HIS A 202 PHE 0.020 0.002 PHE D 86 TYR 0.027 0.002 TYR D 54 ARG 0.006 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.839 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2028 time to fit residues: 31.5378 Evaluate side-chains 95 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7949 Z= 0.141 Angle : 0.493 8.618 10781 Z= 0.241 Chirality : 0.041 0.191 1243 Planarity : 0.004 0.039 1336 Dihedral : 9.471 57.958 1107 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.24 % Allowed : 8.38 % Favored : 91.38 % 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: 0.39 (0.28), residues: 975 helix: 1.14 (0.23), residues: 549 sheet: -0.30 (0.61), residues: 71 loop : -0.95 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 276 HIS 0.004 0.001 HIS B 242 PHE 0.010 0.001 PHE B 188 TYR 0.015 0.001 TYR D 54 ARG 0.004 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.935 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 101 average time/residue: 0.1801 time to fit residues: 25.8052 Evaluate side-chains 96 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0680 time to fit residues: 1.4298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7949 Z= 0.272 Angle : 0.541 9.082 10781 Z= 0.267 Chirality : 0.043 0.168 1243 Planarity : 0.004 0.043 1336 Dihedral : 7.848 59.335 1107 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.20 % Allowed : 10.66 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 975 helix: 1.01 (0.23), residues: 549 sheet: -0.34 (0.64), residues: 70 loop : -1.02 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.014 0.001 PHE D 86 TYR 0.020 0.002 TYR D 54 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 109 average time/residue: 0.2005 time to fit residues: 30.2399 Evaluate side-chains 105 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0766 time to fit residues: 2.3535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7949 Z= 0.262 Angle : 0.526 9.101 10781 Z= 0.261 Chirality : 0.043 0.199 1243 Planarity : 0.004 0.045 1336 Dihedral : 7.216 61.546 1107 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.36 % Allowed : 13.41 % Favored : 86.23 % 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: 0.20 (0.28), residues: 975 helix: 1.00 (0.23), residues: 543 sheet: -0.34 (0.63), residues: 70 loop : -1.04 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.016 0.001 PHE D 86 TYR 0.019 0.002 TYR D 54 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.1902 time to fit residues: 26.7985 Evaluate side-chains 97 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0734 time to fit residues: 1.3982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.379 > 50: distance: 4 - 10: 17.811 distance: 11 - 12: 31.890 distance: 11 - 14: 3.419 distance: 12 - 13: 9.343 distance: 12 - 20: 36.971 distance: 14 - 15: 8.612 distance: 15 - 16: 12.858 distance: 15 - 17: 10.386 distance: 16 - 18: 11.648 distance: 17 - 19: 10.590 distance: 18 - 19: 11.948 distance: 21 - 22: 5.001 distance: 21 - 24: 16.810 distance: 22 - 23: 6.275 distance: 22 - 27: 12.088 distance: 24 - 25: 7.017 distance: 24 - 26: 11.684 distance: 27 - 28: 3.972 distance: 28 - 29: 15.641 distance: 28 - 31: 16.577 distance: 29 - 30: 4.489 distance: 29 - 34: 32.614 distance: 31 - 32: 22.688 distance: 31 - 33: 29.452 distance: 34 - 35: 8.493 distance: 35 - 36: 12.117 distance: 35 - 38: 7.890 distance: 36 - 37: 13.352 distance: 36 - 45: 10.190 distance: 38 - 39: 7.997 distance: 39 - 41: 4.547 distance: 40 - 42: 4.595 distance: 41 - 43: 9.716 distance: 42 - 44: 7.800 distance: 43 - 44: 6.897 distance: 45 - 46: 5.424 distance: 46 - 49: 6.184 distance: 47 - 48: 3.479 distance: 49 - 50: 4.701 distance: 49 - 51: 6.168 distance: 52 - 53: 8.724 distance: 53 - 54: 23.184 distance: 53 - 56: 6.057 distance: 54 - 55: 14.273 distance: 54 - 60: 21.857 distance: 56 - 57: 22.552 distance: 57 - 58: 8.018 distance: 57 - 59: 6.585 distance: 60 - 61: 28.688 distance: 61 - 62: 7.024 distance: 61 - 64: 9.087 distance: 62 - 63: 8.058 distance: 62 - 66: 18.924 distance: 64 - 65: 16.077 distance: 66 - 67: 42.329 distance: 66 - 72: 21.223 distance: 67 - 68: 40.993 distance: 67 - 70: 5.440 distance: 68 - 69: 17.806 distance: 68 - 73: 44.892 distance: 70 - 71: 24.951 distance: 71 - 72: 54.053 distance: 73 - 74: 38.034 distance: 74 - 75: 19.661 distance: 74 - 77: 35.301 distance: 78 - 79: 28.976 distance: 79 - 80: 18.596 distance: 80 - 81: 16.935 distance: 81 - 82: 8.660 distance: 81 - 83: 11.182 distance: 84 - 85: 26.179 distance: 84 - 90: 40.440 distance: 85 - 86: 52.043 distance: 85 - 88: 43.550 distance: 86 - 87: 28.188 distance: 86 - 91: 25.189 distance: 88 - 89: 13.094 distance: 89 - 90: 62.660