Starting phenix.real_space_refine on Sat Dec 9 02:45:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfg_32465/12_2023/7wfg_32465_updated.pdb" } resolution = 4.33 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 64 5.16 5 C 6304 2.51 5 N 1677 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 225": "NH1" <-> "NH2" Residue "H ARG 329": "NH1" <-> "NH2" Residue "H ARG 351": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "L ARG 156": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N ARG 92": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2812 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1236 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1120 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1199 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 646 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 767 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "N" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 909 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 603 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3592 SG CYS I 110 39.258 36.676 84.998 1.00144.09 S ATOM 5818 SG CYS K 108 52.007 42.309 71.485 1.00166.07 S Time building chain proxies: 6.07, per 1000 atoms: 0.62 Number of scatterers: 9836 At special positions: 0 Unit cell: (113.36, 119.6, 121.68, 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 12 26.01 S 64 16.00 O 1779 8.00 N 1677 7.00 C 6304 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 110 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 104 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 114 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 67 " pdb=" SF4 K 301 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 108 " Number of angles added : 18 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 8 sheets defined 35.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'H' and resid 51 through 57 Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.691A pdb=" N GLU H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 124 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 135 through 148 removed outlier: 4.614A pdb=" N PHE H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 195 removed outlier: 4.180A pdb=" N CYS H 179 " --> pdb=" O CYS H 175 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE H 193 " --> pdb=" O TYR H 189 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 214 No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'H' and resid 222 through 227 removed outlier: 4.756A pdb=" N SER H 227 " --> pdb=" O MET H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 236 No H-bonds generated for 'chain 'H' and resid 233 through 236' Processing helix chain 'H' and resid 257 through 277 Processing helix chain 'H' and resid 357 through 364 removed outlier: 4.044A pdb=" N GLN H 363 " --> pdb=" O PHE H 359 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 364 " --> pdb=" O ILE H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 383 removed outlier: 4.367A pdb=" N MET H 378 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 34 removed outlier: 3.871A pdb=" N ASN I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'J' and resid 37 through 44 Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 152 through 154 No H-bonds generated for 'chain 'J' and resid 152 through 154' Processing helix chain 'K' and resid 17 through 30 Processing helix chain 'K' and resid 43 through 47 removed outlier: 3.824A pdb=" N ILE K 46 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K 47 " --> pdb=" O CYS K 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 43 through 47' Processing helix chain 'K' and resid 83 through 96 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'K' and resid 126 through 128 No H-bonds generated for 'chain 'K' and resid 126 through 128' Processing helix chain 'K' and resid 143 through 159 removed outlier: 4.071A pdb=" N ILE K 147 " --> pdb=" O PRO K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 165 Processing helix chain 'L' and resid 98 through 118 removed outlier: 4.048A pdb=" N MET L 108 " --> pdb=" O TYR L 104 " (cutoff:3.500A) Proline residue: L 109 - end of helix Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 140 through 143 removed outlier: 3.849A pdb=" N LEU L 143 " --> pdb=" O PRO L 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 140 through 143' Processing helix chain 'M' and resid 133 through 149 Processing helix chain 'M' and resid 157 through 176 Processing helix chain 'N' and resid 64 through 71 Processing helix chain 'N' and resid 87 through 95 Processing helix chain 'N' and resid 111 through 115 Processing helix chain 'N' and resid 140 through 144 Processing helix chain 'N' and resid 167 through 179 Proline residue: N 176 - end of helix Processing helix chain 'T' and resid 3 through 5 No H-bonds generated for 'chain 'T' and resid 3 through 5' Processing helix chain 'T' and resid 14 through 17 No H-bonds generated for 'chain 'T' and resid 14 through 17' Processing helix chain 'T' and resid 26 through 38 Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 63 through 72 Processing helix chain 'T' and resid 99 through 120 Processing sheet with id= A, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.521A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 29 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 325 through 330 Processing sheet with id= C, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.737A pdb=" N CYS J 85 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE J 31 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS J 87 " --> pdb=" O ILE J 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'J' and resid 64 through 66 Processing sheet with id= E, first strand: chain 'J' and resid 96 through 98 removed outlier: 5.833A pdb=" N THR J 121 " --> pdb=" O ILE J 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= G, first strand: chain 'N' and resid 99 through 103 Processing sheet with id= H, first strand: chain 'O' and resid 140 through 143 removed outlier: 3.926A pdb=" N ASP O 118 " --> pdb=" O LEU O 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY O 131 " --> pdb=" O VAL O 116 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL O 116 " --> pdb=" O GLY O 131 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 852 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: 2.35 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 3991 1.42 - 1.64: 5927 1.64 - 1.86: 82 1.86 - 2.09: 0 2.09 - 2.31: 36 Bond restraints: 10036 Sorted by residual: bond pdb=" C ARG L 152 " pdb=" N LYS L 153 " ideal model delta sigma weight residual 1.332 1.201 0.132 1.40e-02 5.10e+03 8.86e+01 bond pdb=" C GLU I 68 " pdb=" N VAL I 69 " ideal model delta sigma weight residual 1.334 1.265 0.068 1.28e-02 6.10e+03 2.86e+01 bond pdb=" C PRO N 148 " pdb=" N PRO N 149 " ideal model delta sigma weight residual 1.326 1.392 -0.065 1.44e-02 4.82e+03 2.07e+01 bond pdb=" N ARG N 179 " pdb=" CA ARG N 179 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.62e+01 bond pdb=" N LEU N 175 " pdb=" CA LEU N 175 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 72.25 - 84.75: 36 84.75 - 97.25: 0 97.25 - 109.75: 1332 109.75 - 122.25: 10465 122.25 - 134.75: 1811 Bond angle restraints: 13644 Sorted by residual: angle pdb=" N PRO K 140 " pdb=" CA PRO K 140 " pdb=" C PRO K 140 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.08e+01 angle pdb=" N SER N 177 " pdb=" CA SER N 177 " pdb=" C SER N 177 " ideal model delta sigma weight residual 113.23 104.14 9.09 1.24e+00 6.50e-01 5.37e+01 angle pdb=" N LEU K 37 " pdb=" CA LEU K 37 " pdb=" C LEU K 37 " ideal model delta sigma weight residual 113.02 106.16 6.86 1.20e+00 6.94e-01 3.27e+01 angle pdb=" N PRO L 109 " pdb=" CA PRO L 109 " pdb=" C PRO L 109 " ideal model delta sigma weight residual 110.70 117.06 -6.36 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASN N 181 " pdb=" CA ASN N 181 " pdb=" C ASN N 181 " ideal model delta sigma weight residual 114.39 107.58 6.81 1.45e+00 4.76e-01 2.21e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 5624 14.90 - 29.80: 312 29.80 - 44.70: 96 44.70 - 59.60: 26 59.60 - 74.51: 2 Dihedral angle restraints: 6060 sinusoidal: 2097 harmonic: 3963 Sorted by residual: dihedral pdb=" CA THR K 117 " pdb=" C THR K 117 " pdb=" N ASP K 118 " pdb=" CA ASP K 118 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLY H 218 " pdb=" C GLY H 218 " pdb=" N LEU H 219 " pdb=" CA LEU H 219 " ideal model delta harmonic sigma weight residual 180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG L 152 " pdb=" C ARG L 152 " pdb=" N LYS L 153 " pdb=" CA LYS L 153 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1231 0.070 - 0.139: 265 0.139 - 0.209: 52 0.209 - 0.278: 14 0.278 - 0.348: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA LEU H 32 " pdb=" N LEU H 32 " pdb=" C LEU H 32 " pdb=" CB LEU H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG M 161 " pdb=" N ARG M 161 " pdb=" C ARG M 161 " pdb=" CB ARG M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE I 65 " pdb=" CA ILE I 65 " pdb=" CG1 ILE I 65 " pdb=" CG2 ILE I 65 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1560 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 136 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO K 137 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 137 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 137 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 64 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO H 65 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP J 140 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO J 141 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 141 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 841 2.74 - 3.28: 9665 3.28 - 3.82: 16362 3.82 - 4.36: 18461 4.36 - 4.90: 30580 Nonbonded interactions: 75909 Sorted by model distance: nonbonded pdb=" OE2 GLU H 146 " pdb=" N SER I 50 " model vdw 2.204 2.520 nonbonded pdb=" CB ALA H 165 " pdb=" NH1 ARG I 52 " model vdw 2.248 3.540 nonbonded pdb=" NZ LYS N 128 " pdb=" O PRO O 136 " model vdw 2.257 2.520 nonbonded pdb=" O VAL H 203 " pdb=" OG SER H 257 " model vdw 2.301 2.440 nonbonded pdb=" NH2 ARG H 136 " pdb=" O HIS I 32 " model vdw 2.304 2.520 ... (remaining 75904 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 14.160 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 0.132 10036 Z= 0.365 Angle : 1.008 9.753 13644 Z= 0.593 Chirality : 0.063 0.348 1563 Planarity : 0.007 0.064 1745 Dihedral : 11.464 74.505 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.27 % Favored : 87.48 % Rotamer: Outliers : 1.08 % Allowed : 3.11 % Favored : 95.81 % Cbeta Deviations : 0.08 % 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: -5.06 (0.18), residues: 1214 helix: -3.16 (0.16), residues: 405 sheet: -2.66 (0.48), residues: 93 loop : -3.76 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 PHE 0.016 0.002 PHE H 182 TYR 0.016 0.002 TYR J 57 ARG 0.015 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 262 time to evaluate : 1.134 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 132 " (corrupted residue). Skipping it. 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.2388 time to fit residues: 86.1952 Evaluate side-chains 164 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0853 time to fit residues: 2.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 0.0020 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 48 HIS H 363 GLN I 10 ASN J 54 GLN J 110 GLN M 169 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10036 Z= 0.432 Angle : 0.891 11.118 13644 Z= 0.465 Chirality : 0.051 0.198 1563 Planarity : 0.007 0.077 1745 Dihedral : 6.281 27.468 1452 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 32.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 0.48 % Allowed : 5.74 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.22), residues: 1214 helix: -1.44 (0.22), residues: 422 sheet: -2.72 (0.43), residues: 105 loop : -3.26 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 350 HIS 0.014 0.003 HIS H 23 PHE 0.020 0.002 PHE H 340 TYR 0.017 0.002 TYR O 127 ARG 0.015 0.002 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.117 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 outliers start: 4 outliers final: 3 residues processed: 168 average time/residue: 0.2019 time to fit residues: 49.3716 Evaluate side-chains 127 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0955 time to fit residues: 1.9907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.0980 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10036 Z= 0.246 Angle : 0.682 9.527 13644 Z= 0.348 Chirality : 0.045 0.157 1563 Planarity : 0.006 0.068 1745 Dihedral : 5.553 23.964 1452 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.36 % Allowed : 4.31 % Favored : 95.33 % 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: -3.03 (0.23), residues: 1214 helix: -0.53 (0.24), residues: 436 sheet: -2.76 (0.43), residues: 111 loop : -3.04 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 350 HIS 0.008 0.002 HIS H 155 PHE 0.019 0.002 PHE L 134 TYR 0.019 0.001 TYR K 93 ARG 0.014 0.001 ARG M 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.287 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 outliers start: 3 outliers final: 3 residues processed: 178 average time/residue: 0.2136 time to fit residues: 54.2817 Evaluate side-chains 137 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0865 time to fit residues: 2.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.0050 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10036 Z= 0.347 Angle : 0.775 10.562 13644 Z= 0.400 Chirality : 0.047 0.154 1563 Planarity : 0.006 0.065 1745 Dihedral : 5.987 26.487 1452 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.17 % Favored : 85.75 % Rotamer: Outliers : 0.36 % Allowed : 5.50 % Favored : 94.14 % 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: -2.81 (0.24), residues: 1214 helix: -0.43 (0.24), residues: 429 sheet: -2.87 (0.46), residues: 101 loop : -2.79 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 217 HIS 0.009 0.002 HIS H 23 PHE 0.021 0.002 PHE K 115 TYR 0.032 0.002 TYR K 135 ARG 0.025 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 160 average time/residue: 0.1955 time to fit residues: 45.8615 Evaluate side-chains 125 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0865 time to fit residues: 1.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10036 Z= 0.178 Angle : 0.645 10.490 13644 Z= 0.321 Chirality : 0.045 0.160 1563 Planarity : 0.005 0.064 1745 Dihedral : 5.273 24.959 1452 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.37 % Favored : 88.55 % Rotamer: Outliers : 0.36 % Allowed : 2.63 % Favored : 97.01 % 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: -2.65 (0.24), residues: 1214 helix: -0.29 (0.25), residues: 451 sheet: -2.77 (0.43), residues: 109 loop : -2.75 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 217 HIS 0.005 0.001 HIS H 114 PHE 0.014 0.001 PHE L 126 TYR 0.019 0.001 TYR K 93 ARG 0.011 0.001 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 168 average time/residue: 0.1991 time to fit residues: 48.9054 Evaluate side-chains 136 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0858 time to fit residues: 2.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10036 Z= 0.318 Angle : 0.744 11.953 13644 Z= 0.380 Chirality : 0.047 0.169 1563 Planarity : 0.006 0.064 1745 Dihedral : 5.802 25.593 1452 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.17 % Favored : 85.75 % Rotamer: Outliers : 0.36 % Allowed : 3.83 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1214 helix: -0.41 (0.24), residues: 447 sheet: -2.79 (0.49), residues: 89 loop : -2.72 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 35 HIS 0.008 0.002 HIS H 114 PHE 0.029 0.002 PHE K 115 TYR 0.021 0.002 TYR K 93 ARG 0.006 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 151 average time/residue: 0.1829 time to fit residues: 41.2331 Evaluate side-chains 124 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0875 time to fit residues: 2.0236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.8005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10036 Z= 0.290 Angle : 0.738 11.173 13644 Z= 0.373 Chirality : 0.047 0.180 1563 Planarity : 0.005 0.068 1745 Dihedral : 5.855 25.624 1452 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.84 % Favored : 86.08 % Rotamer: Outliers : 0.36 % Allowed : 2.87 % Favored : 96.77 % 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: -2.71 (0.24), residues: 1214 helix: -0.41 (0.24), residues: 441 sheet: -2.82 (0.47), residues: 99 loop : -2.72 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 247 HIS 0.015 0.003 HIS M 96 PHE 0.029 0.002 PHE K 115 TYR 0.020 0.002 TYR K 93 ARG 0.009 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 150 average time/residue: 0.1824 time to fit residues: 41.1715 Evaluate side-chains 122 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0858 time to fit residues: 2.0264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10036 Z= 0.223 Angle : 0.689 11.037 13644 Z= 0.342 Chirality : 0.046 0.174 1563 Planarity : 0.005 0.060 1745 Dihedral : 5.587 25.691 1452 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.18 % Favored : 86.74 % Rotamer: Outliers : 0.36 % Allowed : 1.79 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1214 helix: -0.39 (0.24), residues: 455 sheet: -2.89 (0.45), residues: 104 loop : -2.65 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 247 HIS 0.006 0.001 HIS H 114 PHE 0.027 0.001 PHE K 115 TYR 0.014 0.001 TYR K 93 ARG 0.007 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 158 average time/residue: 0.2056 time to fit residues: 47.3703 Evaluate side-chains 128 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0847 time to fit residues: 1.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.8703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10036 Z= 0.330 Angle : 0.779 10.310 13644 Z= 0.397 Chirality : 0.048 0.223 1563 Planarity : 0.006 0.061 1745 Dihedral : 6.089 25.979 1452 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.66 % Favored : 85.26 % Rotamer: Outliers : 0.36 % Allowed : 1.91 % Favored : 97.73 % 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: -2.85 (0.24), residues: 1214 helix: -0.60 (0.24), residues: 446 sheet: -2.91 (0.52), residues: 84 loop : -2.77 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 247 HIS 0.011 0.002 HIS H 114 PHE 0.018 0.002 PHE K 115 TYR 0.019 0.002 TYR K 93 ARG 0.009 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 149 average time/residue: 0.1892 time to fit residues: 42.1107 Evaluate side-chains 119 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0860 time to fit residues: 2.0871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.8415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10036 Z= 0.192 Angle : 0.699 10.901 13644 Z= 0.343 Chirality : 0.046 0.161 1563 Planarity : 0.005 0.054 1745 Dihedral : 5.500 25.080 1452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.45 % Favored : 88.47 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.24), residues: 1214 helix: -0.48 (0.24), residues: 458 sheet: -2.85 (0.46), residues: 104 loop : -2.77 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 247 HIS 0.005 0.001 HIS H 155 PHE 0.023 0.001 PHE M 143 TYR 0.028 0.001 TYR H 46 ARG 0.006 0.001 ARG H 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 160 average time/residue: 0.1950 time to fit residues: 46.1618 Evaluate side-chains 137 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0861 time to fit residues: 2.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 108 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043782 restraints weight = 114331.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044481 restraints weight = 82787.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.044903 restraints weight = 63717.900| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10036 Z= 0.182 Angle : 0.694 13.209 13644 Z= 0.335 Chirality : 0.046 0.157 1563 Planarity : 0.005 0.052 1745 Dihedral : 5.198 24.828 1452 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.29 % Favored : 88.63 % Rotamer: Outliers : 0.36 % Allowed : 0.96 % Favored : 98.68 % 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: -2.50 (0.24), residues: 1214 helix: -0.25 (0.25), residues: 449 sheet: -2.46 (0.51), residues: 94 loop : -2.65 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 247 HIS 0.008 0.001 HIS J 125 PHE 0.020 0.001 PHE M 143 TYR 0.019 0.001 TYR H 46 ARG 0.007 0.001 ARG I 17 =============================================================================== Job complete usr+sys time: 2068.73 seconds wall clock time: 38 minutes 20.00 seconds (2300.00 seconds total)