Starting phenix.real_space_refine on Thu Jan 18 02:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pcq_13325/01_2024/7pcq_13325_neut_updated.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 22 5.16 5 C 4734 2.51 5 N 1246 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7350 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} bond proxies already assigned to first conformer: 1141 Chain: "C" Number of atoms: 1078 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Conformer: "B" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} bond proxies already assigned to first conformer: 1087 Chain: "D" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1111 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 138} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2777 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324} Conformer: "B" Number of residues, atoms: 337, 2777 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324} bond proxies already assigned to first conformer: 2823 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 104 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 104 " occ=0.50 residue: pdb=" N ALYS C 56 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 56 " occ=0.50 residue: pdb=" N ALYS E 232 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 232 " occ=0.50 Time building chain proxies: 6.67, per 1000 atoms: 0.91 Number of scatterers: 7350 At special positions: 0 Unit cell: (74.98, 99.104, 97.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 22 16.00 O 1344 8.00 N 1246 7.00 C 4734 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 2.1 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 5 sheets defined 56.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 5.988A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLY A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 53 through 71 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.856A pdb=" N MET A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 73 through 79' Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.568A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.806A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.637A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 58 through 76 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.510A pdb=" N AARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'C' and resid 4 through 35 removed outlier: 6.071A pdb=" N ALA C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 53 through 71 Processing helix chain 'C' and resid 73 through 79 removed outlier: 3.857A pdb=" N MET C 76 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Proline residue: C 77 - end of helix No H-bonds generated for 'chain 'C' and resid 73 through 79' Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 119 through 136 Processing helix chain 'D' and resid 5 through 17 removed outlier: 3.730A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 36 through 45 removed outlier: 3.889A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 58 through 76 Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.603A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU D 121 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 141 Processing helix chain 'E' and resid 129 through 132 No H-bonds generated for 'chain 'E' and resid 129 through 132' Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 270 through 284 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 288 through 301 removed outlier: 3.516A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 331 removed outlier: 4.407A pdb=" N ALA E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 451 through 459 removed outlier: 3.747A pdb=" N LYS E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 148 through 151 removed outlier: 6.882A pdb=" N ARG E 224 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU E 211 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER E 226 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 209 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 153 through 156 removed outlier: 4.843A pdb=" N VAL E 200 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 239 through 242 Processing sheet with id= D, first strand: chain 'E' and resid 346 through 348 removed outlier: 4.126A pdb=" N ILE E 371 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER E 406 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 417 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR E 404 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 350 through 353 removed outlier: 5.709A pdb=" N HIS E 434 " --> pdb=" O TRP E 392 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TRP E 392 " --> pdb=" O HIS E 434 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1148 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: 2.01 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 2475 1.37 - 1.55: 5010 1.55 - 1.72: 14 1.72 - 1.90: 38 1.90 - 2.08: 16 Bond restraints: 7553 Sorted by residual: bond pdb=" CA SER E 169 " pdb=" CB SER E 169 " ideal model delta sigma weight residual 1.527 1.465 0.062 1.36e-02 5.41e+03 2.07e+01 bond pdb=" C VAL D 109 " pdb=" O VAL D 109 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.74e+01 bond pdb=" N VAL E 356 " pdb=" CA VAL E 356 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.62e+01 bond pdb=" N VAL E 234 " pdb=" CA VAL E 234 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.11e-02 8.12e+03 1.34e+01 bond pdb=" C3D HEM A 201 " pdb=" CAD HEM A 201 " ideal model delta sigma weight residual 1.544 1.472 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 7548 not shown) Histogram of bond angle deviations from ideal: 87.51 - 105.12: 185 105.12 - 122.73: 8811 122.73 - 140.35: 1289 140.35 - 157.96: 0 157.96 - 175.58: 8 Bond angle restraints: 10293 Sorted by residual: angle pdb=" CA GLN D 127 " pdb=" C GLN D 127 " pdb=" O GLN D 127 " ideal model delta sigma weight residual 120.55 115.25 5.30 1.06e+00 8.90e-01 2.50e+01 angle pdb=" CA GLN B 127 " pdb=" C GLN B 127 " pdb=" O GLN B 127 " ideal model delta sigma weight residual 120.55 115.29 5.26 1.06e+00 8.90e-01 2.46e+01 angle pdb=" N ASP E 364 " pdb=" CA ASP E 364 " pdb=" C ASP E 364 " ideal model delta sigma weight residual 111.28 105.97 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" CA PHE C 43 " pdb=" C PHE C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 117.78 122.72 -4.94 1.06e+00 8.90e-01 2.17e+01 angle pdb=" CA PHE A 43 " pdb=" C PHE A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 117.78 122.69 -4.91 1.06e+00 8.90e-01 2.14e+01 ... (remaining 10288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4092 17.93 - 35.85: 263 35.85 - 53.78: 57 53.78 - 71.71: 10 71.71 - 89.63: 13 Dihedral angle restraints: 4435 sinusoidal: 1762 harmonic: 2673 Sorted by residual: dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -0.00 -85.15 85.15 2 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" C2C HEM C 201 " pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " pdb=" CBC HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 -72.45 72.45 2 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" C2B HEM C 201 " pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " pdb=" CBB HEM C 201 " ideal model delta sinusoidal sigma weight residual 180.00 109.92 70.08 2 1.00e+01 1.00e-02 4.24e+01 ... (remaining 4432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 505 0.062 - 0.123: 342 0.123 - 0.185: 219 0.185 - 0.246: 40 0.246 - 0.307: 8 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA VAL E 176 " pdb=" N VAL E 176 " pdb=" C VAL E 176 " pdb=" CB VAL E 176 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ARG E 130 " pdb=" N ARG E 130 " pdb=" C ARG E 130 " pdb=" CB ARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1111 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 231 " 0.027 2.00e-02 2.50e+03 5.45e-02 2.98e+01 pdb=" C THR E 231 " -0.094 2.00e-02 2.50e+03 pdb=" O THR E 231 " 0.035 2.00e-02 2.50e+03 pdb=" N BLYS E 232 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG B 104 " -0.026 2.00e-02 2.50e+03 5.42e-02 2.93e+01 pdb=" C AARG B 104 " 0.094 2.00e-02 2.50e+03 pdb=" O AARG B 104 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU B 105 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 266 " 0.026 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS E 266 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS E 266 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE E 267 " 0.032 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 4157 3.03 - 3.49: 7736 3.49 - 3.96: 12703 3.96 - 4.43: 14943 4.43 - 4.90: 22486 Nonbonded interactions: 62025 Sorted by model distance: nonbonded pdb=" N THR A 118 " pdb=" O THR A 118 " model vdw 2.557 2.496 nonbonded pdb=" N THR C 118 " pdb=" O THR C 118 " model vdw 2.557 2.496 nonbonded pdb=" O TYR C 140 " pdb=" C ARG C 141 " model vdw 2.557 3.270 nonbonded pdb=" O TYR D 35 " pdb=" OG1 THR D 38 " model vdw 2.564 2.440 nonbonded pdb=" O TYR E 391 " pdb=" N HIS E 434 " model vdw 2.567 2.520 ... (remaining 62020 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 55 or resid 57 through 141 or resid 201)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 141 or resid 201)) } ncs_group { reference = (chain 'B' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 103 or resid 105 through 119 or (re \ sid 120 through 121 and (name N or name CA or name C or name O or name CB )) or \ resid 122 through 146 or resid 201)) selection = (chain 'D' and (resid 1 through 103 or resid 105 through 146 or resid 201)) } 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=0.00 max=1.00 mean=0.99 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: 2.200 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: 0.000 Extract box with map and model: 9.970 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.013 0.089 7553 Z= 0.841 Angle : 1.548 11.328 10293 Z= 1.156 Chirality : 0.098 0.307 1114 Planarity : 0.008 0.055 1298 Dihedral : 13.616 89.634 2707 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.78 % Allowed : 5.58 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.27), residues: 910 helix: 2.24 (0.22), residues: 525 sheet: -0.47 (0.57), residues: 78 loop : -0.33 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 14 HIS 0.005 0.001 HIS C 122 PHE 0.010 0.002 PHE E 225 TYR 0.015 0.002 TYR E 251 ARG 0.007 0.001 ARG E 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8609 (tt0) cc_final: 0.8055 (tt0) REVERT: A 39 THR cc_start: 0.8882 (p) cc_final: 0.7824 (p) REVERT: B 7 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 35 TYR cc_start: 0.8799 (m-80) cc_final: 0.8596 (m-10) REVERT: B 47 ASP cc_start: 0.8397 (t0) cc_final: 0.8156 (t0) REVERT: B 98 VAL cc_start: 0.9513 (t) cc_final: 0.9114 (p) REVERT: B 105 LEU cc_start: 0.9260 (mt) cc_final: 0.9060 (mt) REVERT: B 108 ASN cc_start: 0.9230 (m-40) cc_final: 0.8907 (t0) REVERT: B 127 GLN cc_start: 0.8895 (tt0) cc_final: 0.8234 (tm-30) REVERT: B 131 GLN cc_start: 0.8995 (mm110) cc_final: 0.8478 (mm110) REVERT: C 14 TRP cc_start: 0.8183 (t-100) cc_final: 0.7827 (t-100) REVERT: D 31 LEU cc_start: 0.9406 (tp) cc_final: 0.9200 (tt) REVERT: D 38 THR cc_start: 0.8975 (p) cc_final: 0.8725 (p) outliers start: 5 outliers final: 2 residues processed: 175 average time/residue: 0.2201 time to fit residues: 49.8993 Evaluate side-chains 99 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS B 63 HIS C 58 HIS ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7553 Z= 0.234 Angle : 0.601 6.817 10293 Z= 0.303 Chirality : 0.041 0.162 1114 Planarity : 0.004 0.034 1298 Dihedral : 8.607 84.614 1007 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.34 % Allowed : 13.12 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.60 (0.27), residues: 910 helix: 2.78 (0.21), residues: 525 sheet: -0.10 (0.52), residues: 97 loop : 0.43 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 14 HIS 0.008 0.001 HIS E 369 PHE 0.014 0.002 PHE A 117 TYR 0.010 0.001 TYR E 420 ARG 0.006 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8665 (mt-10) REVERT: B 127 GLN cc_start: 0.9054 (tt0) cc_final: 0.8441 (tm-30) REVERT: B 131 GLN cc_start: 0.9095 (mm110) cc_final: 0.8792 (mm110) REVERT: D 101 GLU cc_start: 0.8147 (tp30) cc_final: 0.7730 (tp30) REVERT: E 155 MET cc_start: 0.8213 (mmm) cc_final: 0.7928 (mmp) REVERT: E 254 MET cc_start: 0.7936 (ttt) cc_final: 0.7685 (ttt) outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 0.1896 time to fit residues: 27.9963 Evaluate side-chains 86 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 108 ASN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7553 Z= 0.306 Angle : 0.617 8.530 10293 Z= 0.304 Chirality : 0.040 0.151 1114 Planarity : 0.004 0.034 1298 Dihedral : 8.624 89.653 1004 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.60 % Allowed : 13.25 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.63 (0.28), residues: 910 helix: 2.72 (0.22), residues: 525 sheet: 0.11 (0.52), residues: 97 loop : 0.56 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 14 HIS 0.006 0.001 HIS E 369 PHE 0.013 0.001 PHE E 178 TYR 0.010 0.001 TYR E 310 ARG 0.004 0.001 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8571 (mt-10) REVERT: B 127 GLN cc_start: 0.9127 (tt0) cc_final: 0.8562 (tm-30) REVERT: B 131 GLN cc_start: 0.9073 (mm110) cc_final: 0.8717 (mm110) REVERT: E 155 MET cc_start: 0.8215 (mmm) cc_final: 0.7872 (mmp) REVERT: E 254 MET cc_start: 0.7854 (ttt) cc_final: 0.7634 (ttt) REVERT: E 375 MET cc_start: 0.9050 (tpp) cc_final: 0.8789 (tpp) outliers start: 19 outliers final: 15 residues processed: 87 average time/residue: 0.1949 time to fit residues: 23.3938 Evaluate side-chains 86 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 382 MET Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 108 ASN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 7553 Z= 0.318 Angle : 0.634 9.596 10293 Z= 0.305 Chirality : 0.040 0.191 1114 Planarity : 0.004 0.035 1298 Dihedral : 8.713 88.417 1004 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.25 % Allowed : 12.86 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.53 (0.28), residues: 910 helix: 2.68 (0.22), residues: 519 sheet: 0.11 (0.51), residues: 98 loop : 0.47 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 14 HIS 0.004 0.001 HIS E 369 PHE 0.014 0.002 PHE E 178 TYR 0.011 0.001 TYR B 35 ARG 0.007 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 7 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 39 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: B 127 GLN cc_start: 0.9099 (tt0) cc_final: 0.8540 (tm-30) REVERT: B 131 GLN cc_start: 0.9107 (mm110) cc_final: 0.8756 (mm110) REVERT: C 32 MET cc_start: 0.7980 (mmm) cc_final: 0.7008 (mmm) REVERT: E 155 MET cc_start: 0.8286 (mmm) cc_final: 0.7888 (mmp) REVERT: E 254 MET cc_start: 0.7802 (ttt) cc_final: 0.7546 (ttt) REVERT: E 375 MET cc_start: 0.9182 (tpp) cc_final: 0.8961 (tpp) outliers start: 24 outliers final: 17 residues processed: 87 average time/residue: 0.1971 time to fit residues: 23.5919 Evaluate side-chains 87 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 382 MET Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 63 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7553 Z= 0.199 Angle : 0.580 9.645 10293 Z= 0.283 Chirality : 0.039 0.175 1114 Planarity : 0.004 0.037 1298 Dihedral : 8.505 89.248 1004 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.82 % Allowed : 13.77 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.67 (0.28), residues: 910 helix: 2.83 (0.22), residues: 517 sheet: 0.24 (0.53), residues: 98 loop : 0.44 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.003 0.001 HIS D 116 PHE 0.009 0.001 PHE E 418 TYR 0.011 0.001 TYR C 140 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8559 (mt-10) REVERT: B 127 GLN cc_start: 0.9035 (tt0) cc_final: 0.8500 (tm-30) REVERT: B 131 GLN cc_start: 0.9012 (mm110) cc_final: 0.8812 (mm110) REVERT: D 101 GLU cc_start: 0.8056 (tp30) cc_final: 0.7535 (tp30) REVERT: D 104 ARG cc_start: 0.8843 (mtm110) cc_final: 0.8383 (ptm-80) REVERT: E 124 MET cc_start: 0.5590 (mmm) cc_final: 0.4555 (tmm) REVERT: E 155 MET cc_start: 0.8351 (mmm) cc_final: 0.7972 (mmp) REVERT: E 254 MET cc_start: 0.7724 (ttt) cc_final: 0.7420 (ttt) REVERT: E 396 MET cc_start: 0.8761 (tpp) cc_final: 0.8548 (tpp) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.2045 time to fit residues: 24.0953 Evaluate side-chains 83 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 382 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7553 Z= 0.235 Angle : 0.593 10.261 10293 Z= 0.287 Chirality : 0.038 0.144 1114 Planarity : 0.004 0.037 1298 Dihedral : 8.474 89.519 1004 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.60 % Allowed : 13.64 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.63 (0.28), residues: 910 helix: 2.79 (0.22), residues: 517 sheet: 0.31 (0.53), residues: 98 loop : 0.41 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 14 HIS 0.003 0.001 HIS C 72 PHE 0.010 0.001 PHE E 225 TYR 0.012 0.001 TYR C 140 ARG 0.008 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 GLU cc_start: 0.9132 (pm20) cc_final: 0.8897 (pm20) REVERT: B 7 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8597 (mt-10) REVERT: B 127 GLN cc_start: 0.9061 (tt0) cc_final: 0.8562 (tm-30) REVERT: E 124 MET cc_start: 0.5649 (mmm) cc_final: 0.4876 (tmm) REVERT: E 155 MET cc_start: 0.8348 (mmm) cc_final: 0.7984 (mmp) REVERT: E 254 MET cc_start: 0.7630 (ttt) cc_final: 0.7423 (ttt) REVERT: E 382 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7537 (mpp) outliers start: 19 outliers final: 14 residues processed: 86 average time/residue: 0.2082 time to fit residues: 24.3652 Evaluate side-chains 86 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain E residue 382 MET Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 52.9926 > 50: distance: 90 - 108: 3.275 distance: 94 - 116: 4.099 distance: 98 - 123: 5.999 distance: 104 - 129: 4.188 distance: 119 - 144: 5.356 distance: 120 - 121: 3.510 distance: 126 - 149: 5.482 distance: 127 - 128: 3.342 distance: 133 - 134: 3.210 distance: 133 - 135: 5.240 distance: 138 - 144: 3.467 distance: 139 - 169: 7.650 distance: 141 - 142: 5.459 distance: 145 - 148: 3.790 distance: 146 - 147: 5.502 distance: 147 - 180: 19.681 distance: 150 - 153: 4.375 distance: 154 - 155: 5.038 distance: 154 - 156: 5.933 distance: 156 - 158: 3.297 distance: 157 - 158: 6.936 distance: 159 - 160: 3.088 distance: 160 - 161: 4.214 distance: 160 - 163: 3.831 distance: 161 - 162: 7.310 distance: 161 - 169: 5.024 distance: 163 - 164: 3.905 distance: 166 - 168: 3.227 distance: 169 - 170: 7.660 distance: 170 - 171: 14.120 distance: 170 - 173: 6.503 distance: 171 - 172: 8.893 distance: 171 - 180: 9.721 distance: 173 - 174: 3.264 distance: 174 - 175: 3.055 distance: 174 - 176: 4.357 distance: 175 - 177: 4.336 distance: 176 - 178: 3.144 distance: 177 - 179: 3.876 distance: 180 - 181: 52.993 distance: 181 - 182: 15.454 distance: 182 - 183: 6.023 distance: 182 - 184: 11.359