Starting phenix.real_space_refine on Sat Nov 18 03:24:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bpz_7128/11_2023/6bpz_7128.pdb" } resolution = 3.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 14124 2.51 5 N 3537 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1671": "NH1" <-> "NH2" Residue "A ARG 1674": "NH1" <-> "NH2" Residue "A ARG 1724": "NH1" <-> "NH2" Residue "A ARG 1728": "NH1" <-> "NH2" Residue "A PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2040": "NH1" <-> "NH2" Residue "A ARG 2126": "NH1" <-> "NH2" Residue "A ARG 2135": "NH1" <-> "NH2" Residue "A ARG 2169": "NH1" <-> "NH2" Residue "A PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2318": "NH1" <-> "NH2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A ARG 2402": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "A ARG 2502": "NH1" <-> "NH2" Residue "A ARG 2514": "NH1" <-> "NH2" Residue "A ARG 2534": "NH1" <-> "NH2" Residue "B PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1176": "NH1" <-> "NH2" Residue "B ARG 1204": "NH1" <-> "NH2" Residue "B ARG 1671": "NH1" <-> "NH2" Residue "B ARG 1674": "NH1" <-> "NH2" Residue "B ARG 1724": "NH1" <-> "NH2" Residue "B ARG 1728": "NH1" <-> "NH2" Residue "B PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2040": "NH1" <-> "NH2" Residue "B ARG 2126": "NH1" <-> "NH2" Residue "B ARG 2135": "NH1" <-> "NH2" Residue "B ARG 2169": "NH1" <-> "NH2" Residue "B PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2318": "NH1" <-> "NH2" Residue "B ARG 2377": "NH1" <-> "NH2" Residue "B ARG 2402": "NH1" <-> "NH2" Residue "B ARG 2406": "NH1" <-> "NH2" Residue "B ARG 2502": "NH1" <-> "NH2" Residue "B ARG 2514": "NH1" <-> "NH2" Residue "B ARG 2534": "NH1" <-> "NH2" Residue "C PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1176": "NH1" <-> "NH2" Residue "C ARG 1204": "NH1" <-> "NH2" Residue "C ARG 1671": "NH1" <-> "NH2" Residue "C ARG 1674": "NH1" <-> "NH2" Residue "C ARG 1724": "NH1" <-> "NH2" Residue "C ARG 1728": "NH1" <-> "NH2" Residue "C PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2040": "NH1" <-> "NH2" Residue "C ARG 2126": "NH1" <-> "NH2" Residue "C ARG 2135": "NH1" <-> "NH2" Residue "C ARG 2169": "NH1" <-> "NH2" Residue "C PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2318": "NH1" <-> "NH2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C ARG 2402": "NH1" <-> "NH2" Residue "C ARG 2406": "NH1" <-> "NH2" Residue "C ARG 2502": "NH1" <-> "NH2" Residue "C ARG 2514": "NH1" <-> "NH2" Residue "C ARG 2534": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21453 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7151 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 864} Chain breaks: 12 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'UNK:plan-1': 59, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7151 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 864} Chain breaks: 12 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'UNK:plan-1': 59, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 7151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7151 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 864} Chain breaks: 12 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'UNK:plan-1': 59, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 91 Time building chain proxies: 11.20, per 1000 atoms: 0.52 Number of scatterers: 21453 At special positions: 0 Unit cell: (186.43, 174.07, 153.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3681 8.00 N 3537 7.00 C 14124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2437 " - pdb=" SG CYS A2441 " distance=2.03 Simple disulfide: pdb=" SG CYS B2437 " - pdb=" SG CYS B2441 " distance=2.03 Simple disulfide: pdb=" SG CYS C2437 " - pdb=" SG CYS C2441 " distance=2.03 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: 8.48 Conformation dependent library (CDL) restraints added in 3.8 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5202 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 72.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 1150 through 1159 Processing helix chain 'A' and resid 1160 through 1173 removed outlier: 3.530A pdb=" N LEU A1164 " --> pdb=" O TYR A1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1193 removed outlier: 3.616A pdb=" N LEU A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.535A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1232 removed outlier: 4.148A pdb=" N VAL A1208 " --> pdb=" O ARG A1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A1213 " --> pdb=" O LEU A1209 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1220 " --> pdb=" O TYR A1216 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1298 removed outlier: 3.568A pdb=" N PHE A1289 " --> pdb=" O ILE A1285 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1290 " --> pdb=" O CYS A1286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1292 " --> pdb=" O PHE A1288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1307 through 1315 Processing helix chain 'A' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN A1336 " --> pdb=" O ASN A1332 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU A1414 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A1415 " --> pdb=" O TYR A1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1411 through 1415' Processing helix chain 'A' and resid 1502 through 1511 Processing helix chain 'A' and resid 1513 through 1519 removed outlier: 3.589A pdb=" N UNK A1517 " --> pdb=" O UNK A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1619 removed outlier: 4.017A pdb=" N UNK A1607 " --> pdb=" O UNK A1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK A1608 " --> pdb=" O UNK A1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK A1618 " --> pdb=" O UNK A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1640 removed outlier: 3.773A pdb=" N UNK A1632 " --> pdb=" O UNK A1628 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK A1633 " --> pdb=" O UNK A1629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK A1634 " --> pdb=" O UNK A1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK A1635 " --> pdb=" O UNK A1631 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N UNK A1639 " --> pdb=" O UNK A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1667 removed outlier: 4.297A pdb=" N PHE A1665 " --> pdb=" O GLU A1661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1666 " --> pdb=" O ALA A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 removed outlier: 3.652A pdb=" N ALA A1678 " --> pdb=" O ARG A1674 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A1686 " --> pdb=" O CYS A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1687 through 1703 removed outlier: 4.012A pdb=" N ILE A1696 " --> pdb=" O TYR A1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1747 Processing helix chain 'A' and resid 1783 through 1803 Processing helix chain 'A' and resid 1957 through 1960 Processing helix chain 'A' and resid 1961 through 1967 Processing helix chain 'A' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE A1991 " --> pdb=" O ASP A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2040 Processing helix chain 'A' and resid 2043 through 2063 removed outlier: 4.075A pdb=" N VAL A2055 " --> pdb=" O VAL A2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A2056 " --> pdb=" O VAL A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2142 Processing helix chain 'A' and resid 2148 through 2175 removed outlier: 3.626A pdb=" N TYR A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS A2188 " --> pdb=" O LYS A2184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A2195 " --> pdb=" O MET A2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A2197 " --> pdb=" O GLY A2193 " (cutoff:3.500A) Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2252 through 2263 Processing helix chain 'A' and resid 2266 through 2274 Processing helix chain 'A' and resid 2275 through 2276 No H-bonds generated for 'chain 'A' and resid 2275 through 2276' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2327 through 2330 Processing helix chain 'A' and resid 2348 through 2357 Processing helix chain 'A' and resid 2358 through 2360 No H-bonds generated for 'chain 'A' and resid 2358 through 2360' Processing helix chain 'A' and resid 2467 through 2485 Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'B' and resid 1150 through 1159 Processing helix chain 'B' and resid 1160 through 1173 removed outlier: 3.530A pdb=" N LEU B1164 " --> pdb=" O TYR B1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B1166 " --> pdb=" O PHE B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1193 removed outlier: 3.615A pdb=" N LEU B1182 " --> pdb=" O SER B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1199 removed outlier: 3.536A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1232 removed outlier: 4.149A pdb=" N VAL B1208 " --> pdb=" O ARG B1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B1213 " --> pdb=" O LEU B1209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B1220 " --> pdb=" O TYR B1216 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1298 removed outlier: 3.566A pdb=" N PHE B1289 " --> pdb=" O ILE B1285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B1290 " --> pdb=" O CYS B1286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B1291 " --> pdb=" O PHE B1287 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B1292 " --> pdb=" O PHE B1288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B1298 " --> pdb=" O ARG B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1306 Processing helix chain 'B' and resid 1307 through 1315 Processing helix chain 'B' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN B1336 " --> pdb=" O ASN B1332 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B1359 " --> pdb=" O LYS B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU B1414 " --> pdb=" O ASP B1411 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B1415 " --> pdb=" O TYR B1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1411 through 1415' Processing helix chain 'B' and resid 1502 through 1511 Processing helix chain 'B' and resid 1513 through 1519 removed outlier: 3.589A pdb=" N UNK B1517 " --> pdb=" O UNK B1513 " (cutoff:3.500A) Processing helix chain 'B' and resid 1603 through 1619 removed outlier: 4.017A pdb=" N UNK B1607 " --> pdb=" O UNK B1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK B1608 " --> pdb=" O UNK B1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK B1618 " --> pdb=" O UNK B1614 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1640 removed outlier: 3.772A pdb=" N UNK B1632 " --> pdb=" O UNK B1628 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK B1633 " --> pdb=" O UNK B1629 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N UNK B1634 " --> pdb=" O UNK B1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK B1635 " --> pdb=" O UNK B1631 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N UNK B1639 " --> pdb=" O UNK B1635 " (cutoff:3.500A) Processing helix chain 'B' and resid 1661 through 1667 removed outlier: 4.296A pdb=" N PHE B1665 " --> pdb=" O GLU B1661 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B1666 " --> pdb=" O ALA B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1686 removed outlier: 3.653A pdb=" N ALA B1678 " --> pdb=" O ARG B1674 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS B1686 " --> pdb=" O CYS B1682 " (cutoff:3.500A) Processing helix chain 'B' and resid 1687 through 1703 removed outlier: 4.013A pdb=" N ILE B1696 " --> pdb=" O TYR B1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1701 " --> pdb=" O LEU B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL B1712 " --> pdb=" O LEU B1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B1713 " --> pdb=" O VAL B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1747 Processing helix chain 'B' and resid 1783 through 1803 Processing helix chain 'B' and resid 1957 through 1960 Processing helix chain 'B' and resid 1961 through 1967 Processing helix chain 'B' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE B1991 " --> pdb=" O ASP B1987 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2040 Processing helix chain 'B' and resid 2043 through 2063 removed outlier: 4.076A pdb=" N VAL B2055 " --> pdb=" O VAL B2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B2056 " --> pdb=" O VAL B2052 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2100 Processing helix chain 'B' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) Processing helix chain 'B' and resid 2132 through 2142 Processing helix chain 'B' and resid 2148 through 2175 removed outlier: 3.625A pdb=" N TYR B2175 " --> pdb=" O THR B2171 " (cutoff:3.500A) Processing helix chain 'B' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS B2188 " --> pdb=" O LYS B2184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B2195 " --> pdb=" O MET B2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B2197 " --> pdb=" O GLY B2193 " (cutoff:3.500A) Proline residue: B2206 - end of helix Processing helix chain 'B' and resid 2252 through 2263 Processing helix chain 'B' and resid 2266 through 2274 Processing helix chain 'B' and resid 2275 through 2276 No H-bonds generated for 'chain 'B' and resid 2275 through 2276' Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2327 through 2330 Processing helix chain 'B' and resid 2348 through 2357 Processing helix chain 'B' and resid 2358 through 2360 No H-bonds generated for 'chain 'B' and resid 2358 through 2360' Processing helix chain 'B' and resid 2467 through 2485 Processing helix chain 'B' and resid 2500 through 2516 Processing helix chain 'B' and resid 2521 through 2533 Processing helix chain 'B' and resid 2535 through 2543 Processing helix chain 'C' and resid 1150 through 1159 Processing helix chain 'C' and resid 1160 through 1173 removed outlier: 3.529A pdb=" N LEU C1164 " --> pdb=" O TYR C1160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C1166 " --> pdb=" O PHE C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1193 removed outlier: 3.615A pdb=" N LEU C1182 " --> pdb=" O SER C1178 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1199 removed outlier: 3.536A pdb=" N LEU C1199 " --> pdb=" O GLY C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1232 removed outlier: 4.148A pdb=" N VAL C1208 " --> pdb=" O ARG C1204 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C1213 " --> pdb=" O LEU C1209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C1220 " --> pdb=" O TYR C1216 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C1221 " --> pdb=" O ASN C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1298 removed outlier: 3.566A pdb=" N PHE C1289 " --> pdb=" O ILE C1285 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C1290 " --> pdb=" O CYS C1286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1291 " --> pdb=" O PHE C1287 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C1292 " --> pdb=" O PHE C1288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C1298 " --> pdb=" O ARG C1294 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1306 Processing helix chain 'C' and resid 1307 through 1315 Processing helix chain 'C' and resid 1315 through 1364 removed outlier: 3.734A pdb=" N GLN C1336 " --> pdb=" O ASN C1332 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C1359 " --> pdb=" O LYS C1355 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1415 removed outlier: 3.728A pdb=" N LEU C1414 " --> pdb=" O ASP C1411 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C1415 " --> pdb=" O TYR C1412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1411 through 1415' Processing helix chain 'C' and resid 1502 through 1511 Processing helix chain 'C' and resid 1513 through 1519 removed outlier: 3.590A pdb=" N UNK C1517 " --> pdb=" O UNK C1513 " (cutoff:3.500A) Processing helix chain 'C' and resid 1603 through 1619 removed outlier: 4.018A pdb=" N UNK C1607 " --> pdb=" O UNK C1603 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK C1608 " --> pdb=" O UNK C1604 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK C1618 " --> pdb=" O UNK C1614 " (cutoff:3.500A) Processing helix chain 'C' and resid 1619 through 1640 removed outlier: 3.772A pdb=" N UNK C1632 " --> pdb=" O UNK C1628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK C1633 " --> pdb=" O UNK C1629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N UNK C1634 " --> pdb=" O UNK C1630 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK C1635 " --> pdb=" O UNK C1631 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N UNK C1639 " --> pdb=" O UNK C1635 " (cutoff:3.500A) Processing helix chain 'C' and resid 1661 through 1667 removed outlier: 4.297A pdb=" N PHE C1665 " --> pdb=" O GLU C1661 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C1666 " --> pdb=" O ALA C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1686 removed outlier: 3.652A pdb=" N ALA C1678 " --> pdb=" O ARG C1674 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS C1686 " --> pdb=" O CYS C1682 " (cutoff:3.500A) Processing helix chain 'C' and resid 1687 through 1703 removed outlier: 4.013A pdb=" N ILE C1696 " --> pdb=" O TYR C1692 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C1701 " --> pdb=" O LEU C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 removed outlier: 3.509A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1747 Processing helix chain 'C' and resid 1783 through 1803 Processing helix chain 'C' and resid 1957 through 1960 Processing helix chain 'C' and resid 1961 through 1967 Processing helix chain 'C' and resid 1976 through 1995 removed outlier: 4.038A pdb=" N ILE C1991 " --> pdb=" O ASP C1987 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2040 Processing helix chain 'C' and resid 2043 through 2063 removed outlier: 4.076A pdb=" N VAL C2055 " --> pdb=" O VAL C2051 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C2056 " --> pdb=" O VAL C2052 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2115 through 2127 removed outlier: 3.599A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) Processing helix chain 'C' and resid 2132 through 2142 Processing helix chain 'C' and resid 2148 through 2175 removed outlier: 3.625A pdb=" N TYR C2175 " --> pdb=" O THR C2171 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2211 removed outlier: 3.659A pdb=" N LYS C2188 " --> pdb=" O LYS C2184 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C2195 " --> pdb=" O MET C2191 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C2197 " --> pdb=" O GLY C2193 " (cutoff:3.500A) Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2252 through 2263 Processing helix chain 'C' and resid 2266 through 2274 Processing helix chain 'C' and resid 2275 through 2276 No H-bonds generated for 'chain 'C' and resid 2275 through 2276' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2327 through 2330 Processing helix chain 'C' and resid 2348 through 2357 Processing helix chain 'C' and resid 2358 through 2360 No H-bonds generated for 'chain 'C' and resid 2358 through 2360' Processing helix chain 'C' and resid 2467 through 2485 Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2521 through 2533 Processing helix chain 'C' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'A' and resid 2239 through 2243 removed outlier: 3.581A pdb=" N ASP A2225 " --> pdb=" O GLN A2324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE A2286 " --> pdb=" O LEU A2444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 3.784A pdb=" N HIS A2370 " --> pdb=" O LEU A2399 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A2399 " --> pdb=" O HIS A2370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2239 through 2243 removed outlier: 3.582A pdb=" N ASP B2225 " --> pdb=" O GLN B2324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE B2286 " --> pdb=" O LEU B2444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 3.784A pdb=" N HIS B2370 " --> pdb=" O LEU B2399 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B2399 " --> pdb=" O HIS B2370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2239 through 2243 removed outlier: 3.581A pdb=" N ASP C2225 " --> pdb=" O GLN C2324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 3.617A pdb=" N ILE C2286 " --> pdb=" O LEU C2444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 3.783A pdb=" N HIS C2370 " --> pdb=" O LEU C2399 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU C2399 " --> pdb=" O HIS C2370 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 4005 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: 7.62 Time building geometry restraints manager: 8.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5128 1.33 - 1.45: 5024 1.45 - 1.57: 11631 1.57 - 1.69: 0 1.69 - 1.82: 177 Bond restraints: 21960 Sorted by residual: bond pdb=" CG1 ILE B2158 " pdb=" CD1 ILE B2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.87e+00 bond pdb=" CG1 ILE A2158 " pdb=" CD1 ILE A2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.86e+00 bond pdb=" CG1 ILE C2158 " pdb=" CD1 ILE C2158 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.85e+00 bond pdb=" CB LEU A2443 " pdb=" CG LEU A2443 " ideal model delta sigma weight residual 1.530 1.484 0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" CG1 ILE B1695 " pdb=" CD1 ILE B1695 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 ... (remaining 21955 not shown) Histogram of bond angle deviations from ideal: 97.77 - 106.45: 726 106.45 - 115.12: 12839 115.12 - 123.80: 15411 123.80 - 132.47: 745 132.47 - 141.15: 72 Bond angle restraints: 29793 Sorted by residual: angle pdb=" C SER A1148 " pdb=" N TYR A1149 " pdb=" CA TYR A1149 " ideal model delta sigma weight residual 121.54 141.15 -19.61 1.91e+00 2.74e-01 1.05e+02 angle pdb=" C SER C1148 " pdb=" N TYR C1149 " pdb=" CA TYR C1149 " ideal model delta sigma weight residual 121.54 141.12 -19.58 1.91e+00 2.74e-01 1.05e+02 angle pdb=" C SER B1148 " pdb=" N TYR B1149 " pdb=" CA TYR B1149 " ideal model delta sigma weight residual 121.54 141.11 -19.57 1.91e+00 2.74e-01 1.05e+02 angle pdb=" N SER B1148 " pdb=" CA SER B1148 " pdb=" C SER B1148 " ideal model delta sigma weight residual 109.80 121.34 -11.54 1.70e+00 3.46e-01 4.60e+01 angle pdb=" N SER C1148 " pdb=" CA SER C1148 " pdb=" C SER C1148 " ideal model delta sigma weight residual 109.80 121.33 -11.53 1.70e+00 3.46e-01 4.60e+01 ... (remaining 29788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 12079 15.77 - 31.55: 695 31.55 - 47.32: 198 47.32 - 63.09: 12 63.09 - 78.87: 24 Dihedral angle restraints: 13008 sinusoidal: 5034 harmonic: 7974 Sorted by residual: dihedral pdb=" N PHE C2205 " pdb=" C PHE C2205 " pdb=" CA PHE C2205 " pdb=" CB PHE C2205 " ideal model delta harmonic sigma weight residual 122.80 132.69 -9.89 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE A2205 " pdb=" C PHE A2205 " pdb=" CA PHE A2205 " pdb=" CB PHE A2205 " ideal model delta harmonic sigma weight residual 122.80 132.67 -9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE B2205 " pdb=" C PHE B2205 " pdb=" CA PHE B2205 " pdb=" CB PHE B2205 " ideal model delta harmonic sigma weight residual 122.80 132.64 -9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 3243 0.152 - 0.304: 177 0.304 - 0.456: 6 0.456 - 0.607: 0 0.607 - 0.759: 3 Chirality restraints: 3429 Sorted by residual: chirality pdb=" CG LEU B1805 " pdb=" CB LEU B1805 " pdb=" CD1 LEU B1805 " pdb=" CD2 LEU B1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CG LEU A1805 " pdb=" CB LEU A1805 " pdb=" CD1 LEU A1805 " pdb=" CD2 LEU A1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU C1805 " pdb=" CB LEU C1805 " pdb=" CD1 LEU C1805 " pdb=" CD2 LEU C1805 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 3426 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C2542 " 0.034 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP C2542 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C2542 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C2542 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C2542 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C2542 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C2542 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C2542 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C2542 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C2542 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2542 " -0.033 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP A2542 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP A2542 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A2542 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A2542 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A2542 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A2542 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2542 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2542 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A2542 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B2542 " -0.033 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP B2542 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B2542 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B2542 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B2542 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B2542 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B2542 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2542 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2542 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B2542 " -0.008 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5650 2.79 - 3.32: 20717 3.32 - 3.84: 35541 3.84 - 4.37: 40132 4.37 - 4.90: 66407 Nonbonded interactions: 168447 Sorted by model distance: nonbonded pdb=" OH TYR A1970 " pdb=" O ARG A2098 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR B1970 " pdb=" O ARG B2098 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR C1970 " pdb=" O ARG C2098 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR A1184 " pdb=" OD1 ASP A1283 " model vdw 2.288 2.440 nonbonded pdb=" OH TYR C1184 " pdb=" OD1 ASP C1283 " model vdw 2.289 2.440 ... (remaining 168442 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' selection = chain 'B' selection = chain 'C' } 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: 3.130 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: 0.020 Extract box with map and model: 14.490 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 56.610 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 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 : 0.010 0.116 21960 Z= 0.637 Angle : 1.550 19.608 29793 Z= 0.815 Chirality : 0.078 0.759 3429 Planarity : 0.008 0.079 3684 Dihedral : 11.479 78.869 7797 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.94 % Favored : 91.82 % Rotamer: Outliers : 0.14 % Allowed : 8.42 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.66 (0.12), residues: 2457 helix: -3.15 (0.08), residues: 1581 sheet: -1.14 (0.27), residues: 255 loop : -3.04 (0.21), residues: 621 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 603 time to evaluate : 2.546 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 606 average time/residue: 0.3143 time to fit residues: 297.4015 Evaluate side-chains 373 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1807 time to fit residues: 3.5027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 61.5278 > 50: distance: 42 - 64: 7.714 distance: 47 - 73: 4.412 distance: 55 - 84: 4.316 distance: 58 - 64: 7.004 distance: 59 - 92: 5.215 distance: 64 - 65: 5.726 distance: 65 - 66: 6.391 distance: 66 - 67: 10.647 distance: 66 - 73: 3.484 distance: 68 - 69: 5.443 distance: 69 - 70: 3.130 distance: 70 - 71: 4.488 distance: 70 - 72: 7.971 distance: 73 - 74: 9.334 distance: 74 - 75: 11.250 distance: 74 - 77: 8.563 distance: 75 - 76: 16.949 distance: 75 - 84: 5.005 distance: 77 - 78: 11.010 distance: 78 - 79: 14.018 distance: 78 - 80: 5.496 distance: 79 - 81: 6.997 distance: 80 - 82: 7.274 distance: 81 - 83: 6.943 distance: 82 - 83: 3.618 distance: 84 - 85: 9.533 distance: 85 - 86: 8.284 distance: 85 - 88: 8.355 distance: 86 - 87: 5.546 distance: 86 - 92: 14.903 distance: 88 - 89: 12.399 distance: 88 - 90: 11.571 distance: 89 - 91: 14.712 distance: 92 - 93: 7.480 distance: 93 - 94: 10.310 distance: 93 - 96: 6.583 distance: 94 - 95: 10.976 distance: 94 - 98: 10.524 distance: 96 - 97: 21.659 distance: 98 - 99: 10.505 distance: 99 - 100: 11.538 distance: 99 - 102: 7.798 distance: 100 - 101: 25.830 distance: 100 - 107: 8.478 distance: 102 - 103: 9.335 distance: 103 - 104: 7.140 distance: 104 - 105: 3.692 distance: 104 - 106: 5.524 distance: 107 - 108: 34.202 distance: 108 - 109: 46.952 distance: 108 - 111: 26.388 distance: 109 - 110: 21.325 distance: 109 - 119: 54.327 distance: 111 - 112: 10.363 distance: 112 - 113: 3.417 distance: 112 - 114: 5.025 distance: 113 - 115: 4.746 distance: 114 - 116: 5.425 distance: 115 - 117: 4.516 distance: 116 - 117: 7.834 distance: 117 - 118: 5.198 distance: 119 - 120: 12.132 distance: 120 - 121: 39.967 distance: 120 - 123: 20.528 distance: 121 - 122: 31.805 distance: 121 - 125: 27.423 distance: 123 - 124: 9.056 distance: 125 - 126: 11.091 distance: 125 - 131: 13.244 distance: 126 - 127: 8.517 distance: 126 - 129: 19.227 distance: 127 - 128: 4.156 distance: 127 - 132: 10.420 distance: 129 - 130: 8.190 distance: 130 - 131: 19.642 distance: 132 - 133: 5.768 distance: 133 - 134: 3.178 distance: 134 - 135: 13.691 distance: 134 - 141: 6.148 distance: 136 - 137: 3.139 distance: 137 - 138: 10.412 distance: 138 - 139: 7.797 distance: 138 - 140: 6.466 distance: 141 - 142: 6.891 distance: 142 - 143: 7.973 distance: 142 - 145: 4.719 distance: 143 - 144: 16.287 distance: 143 - 149: 4.935 distance: 145 - 146: 7.097 distance: 146 - 147: 10.786 distance: 146 - 148: 4.771 distance: 157 - 177: 3.160