Starting phenix.real_space_refine on Sun Jun 30 23:09:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/06_2024/7pil_13441_updated.pdb" } resolution = 2.5 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= 0.003 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 Mg 32 5.21 5 S 90 5.16 5 C 15852 2.51 5 N 3119 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BE ASP 13": "OD1" <-> "OD2" Residue "BK TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 22480 Number of models: 1 Model: "" Number of chains: 66 Chain: "AA" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "AB" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AC" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AD" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AE" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AF" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AG" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AH" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AI" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AJ" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AK" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AL" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AM" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 461 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AN" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "BA" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BB" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BC" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BD" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BE" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BF" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BG" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BH" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BI" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BJ" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BK" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BL" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BM" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BN" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "H" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1867 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "UU" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 363 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "X" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "AA" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'3PE': 1, 'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AD" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AF" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AI" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BG" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.89, per 1000 atoms: 0.66 Number of scatterers: 22480 At special positions: 0 Unit cell: (138.45, 129.35, 96.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 90 16.00 P 6 15.00 Mg 32 11.99 O 3380 8.00 N 3119 7.00 C 15852 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 3.1 seconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 4 sheets defined 65.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 9 Processing helix chain 'AA' and resid 13 through 36 Processing helix chain 'AB' and resid 4 through 9 Processing helix chain 'AB' and resid 13 through 36 Processing helix chain 'AB' and resid 43 through 50 Processing helix chain 'AC' and resid 4 through 9 Processing helix chain 'AC' and resid 13 through 36 removed outlier: 3.508A pdb=" N VALAC 18 " --> pdb=" O ARGAC 14 " (cutoff:3.500A) Processing helix chain 'AC' and resid 43 through 50 Processing helix chain 'AD' and resid 4 through 10 Processing helix chain 'AD' and resid 13 through 36 Processing helix chain 'AD' and resid 43 through 50 Processing helix chain 'AE' and resid 2 through 10 removed outlier: 4.183A pdb=" N TYRAE 5 " --> pdb=" O SERAE 2 " (cutoff:3.500A) Processing helix chain 'AE' and resid 13 through 36 Processing helix chain 'AE' and resid 43 through 50 Processing helix chain 'AF' and resid 4 through 10 Processing helix chain 'AF' and resid 13 through 37 Processing helix chain 'AF' and resid 43 through 50 Processing helix chain 'AG' and resid 4 through 10 Processing helix chain 'AG' and resid 13 through 37 Processing helix chain 'AG' and resid 43 through 50 Processing helix chain 'AH' and resid 4 through 10 Processing helix chain 'AH' and resid 13 through 36 Processing helix chain 'AH' and resid 43 through 50 Processing helix chain 'AI' and resid 4 through 9 Processing helix chain 'AI' and resid 13 through 37 Processing helix chain 'AI' and resid 43 through 50 Processing helix chain 'AJ' and resid 2 through 10 removed outlier: 4.286A pdb=" N TYRAJ 5 " --> pdb=" O SERAJ 2 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 13 through 36 Processing helix chain 'AJ' and resid 43 through 50 Processing helix chain 'AK' and resid 4 through 9 Processing helix chain 'AK' and resid 13 through 36 Processing helix chain 'AK' and resid 43 through 50 Processing helix chain 'AL' and resid 2 through 10 removed outlier: 4.159A pdb=" N TYRAL 5 " --> pdb=" O SERAL 2 " (cutoff:3.500A) Processing helix chain 'AL' and resid 13 through 36 Processing helix chain 'AL' and resid 43 through 50 Processing helix chain 'AM' and resid 2 through 9 removed outlier: 4.310A pdb=" N TYRAM 5 " --> pdb=" O SERAM 2 " (cutoff:3.500A) Processing helix chain 'AM' and resid 13 through 36 Processing helix chain 'AM' and resid 43 through 50 Processing helix chain 'AN' and resid 5 through 10 Processing helix chain 'AN' and resid 13 through 36 Processing helix chain 'AN' and resid 43 through 50 Processing helix chain 'BA' and resid 13 through 44 Processing helix chain 'BB' and resid 13 through 44 Processing helix chain 'BC' and resid 13 through 44 Processing helix chain 'BD' and resid 13 through 44 Processing helix chain 'BE' and resid 13 through 44 Processing helix chain 'BF' and resid 13 through 44 Processing helix chain 'BG' and resid 13 through 44 Processing helix chain 'BH' and resid 13 through 44 Processing helix chain 'BI' and resid 13 through 44 Processing helix chain 'BJ' and resid 13 through 44 removed outlier: 3.511A pdb=" N VALBJ 22 " --> pdb=" O GLUBJ 18 " (cutoff:3.500A) Processing helix chain 'BK' and resid 13 through 44 Processing helix chain 'BL' and resid 13 through 44 removed outlier: 3.517A pdb=" N SERBL 25 " --> pdb=" O SERBL 21 " (cutoff:3.500A) Processing helix chain 'BM' and resid 13 through 44 Processing helix chain 'BN' and resid 13 through 44 removed outlier: 3.581A pdb=" N SERBN 25 " --> pdb=" O SERBN 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.548A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.176A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.718A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.087A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.874A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.563A pdb=" N TRP L 263 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.503A pdb=" N TRP M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 41' Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 89 through 91 No H-bonds generated for 'chain 'M' and resid 89 through 91' Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.585A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.610A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.755A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'UU' and resid 6 through 29 Processing helix chain 'UU' and resid 32 through 47 Processing helix chain 'X' and resid 16 through 54 Processing helix chain 'X' and resid 56 through 58 No H-bonds generated for 'chain 'X' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.756A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.581A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3228 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: 6.17 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 6439 1.37 - 1.57: 16588 1.57 - 1.78: 15 1.78 - 1.99: 174 1.99 - 2.19: 128 Bond restraints: 23344 Sorted by residual: bond pdb=" O11 CD4 M 405 " pdb=" P2 CD4 M 405 " ideal model delta sigma weight residual 1.508 1.606 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O6 CD4 M 405 " pdb=" P1 CD4 M 405 " ideal model delta sigma weight residual 1.510 1.606 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C35 CD4 M 405 " pdb=" O14 CD4 M 405 " ideal model delta sigma weight residual 1.440 1.346 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4A BPH M 402 " pdb=" NA BPH M 402 " ideal model delta sigma weight residual 1.312 1.384 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C4A BPH L 301 " pdb=" NA BPH L 301 " ideal model delta sigma weight residual 1.312 1.383 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 23339 not shown) Histogram of bond angle deviations from ideal: 84.27 - 99.19: 129 99.19 - 114.10: 13431 114.10 - 129.02: 17821 129.02 - 143.94: 573 143.94 - 158.85: 98 Bond angle restraints: 32052 Sorted by residual: angle pdb=" C3 UQ1 L 303 " pdb=" O3 UQ1 L 303 " pdb=" CM3 UQ1 L 303 " ideal model delta sigma weight residual 115.37 129.84 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C6 UQ1 L 303 " pdb=" C7 UQ1 L 303 " pdb=" C8 UQ1 L 303 " ideal model delta sigma weight residual 110.15 121.69 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C4 U10 M 404 " pdb=" O4 U10 M 404 " pdb=" C4M U10 M 404 " ideal model delta sigma weight residual 120.00 130.35 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C3 U10 M 404 " pdb=" O3 U10 M 404 " pdb=" C3M U10 M 404 " ideal model delta sigma weight residual 120.00 130.17 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA TRPBK 47 " pdb=" CB TRPBK 47 " pdb=" CG TRPBK 47 " ideal model delta sigma weight residual 113.60 120.01 -6.41 1.90e+00 2.77e-01 1.14e+01 ... (remaining 32047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 12336 35.95 - 71.91: 268 71.91 - 107.86: 40 107.86 - 143.81: 13 143.81 - 179.77: 9 Dihedral angle restraints: 12666 sinusoidal: 6041 harmonic: 6625 Sorted by residual: dihedral pdb=" C1 BCLAI 101 " pdb=" C2 BCLAI 101 " pdb=" C3 BCLAI 101 " pdb=" C5 BCLAI 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.23 -179.77 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAC 102 " pdb=" C2 BCLAC 102 " pdb=" C3 BCLAC 102 " pdb=" C5 BCLAC 102 " ideal model delta sinusoidal sigma weight residual 180.00 1.82 178.18 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAB 101 " pdb=" C2 BCLAB 101 " pdb=" C3 BCLAB 101 " pdb=" C5 BCLAB 101 " ideal model delta sinusoidal sigma weight residual 180.00 1.87 178.13 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 12663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2110 0.044 - 0.087: 773 0.087 - 0.131: 203 0.131 - 0.174: 60 0.174 - 0.218: 10 Chirality restraints: 3156 Sorted by residual: chirality pdb=" C2C BPH M 402 " pdb=" C1C BPH M 402 " pdb=" C3C BPH M 402 " pdb=" CMC BPH M 402 " both_signs ideal model delta sigma weight residual False -2.81 -2.59 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3B LMTAA1003 " pdb=" C2B LMTAA1003 " pdb=" C4B LMTAA1003 " pdb=" O3B LMTAA1003 " both_signs ideal model delta sigma weight residual False 2.50 2.29 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C3B LMT X 101 " pdb=" C2B LMT X 101 " pdb=" C4B LMT X 101 " pdb=" O3B LMT X 101 " both_signs ideal model delta sigma weight residual False 2.50 2.30 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 3153 not shown) Planarity restraints: 3928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCLAL1001 " 0.075 1.50e-02 4.44e+03 6.30e-02 8.81e+01 pdb=" C2 BCLAL1001 " -0.094 1.50e-02 4.44e+03 pdb=" C3 BCLAL1001 " -0.040 1.50e-02 4.44e+03 pdb=" C4 BCLAL1001 " -0.002 1.50e-02 4.44e+03 pdb=" C5 BCLAL1001 " 0.062 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAD 102 " -0.070 1.50e-02 4.44e+03 5.86e-02 7.63e+01 pdb=" C2 BCLAD 102 " 0.091 1.50e-02 4.44e+03 pdb=" C3 BCLAD 102 " 0.032 1.50e-02 4.44e+03 pdb=" C4 BCLAD 102 " 0.002 1.50e-02 4.44e+03 pdb=" C5 BCLAD 102 " -0.055 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAM1001 " 0.068 1.50e-02 4.44e+03 5.76e-02 7.37e+01 pdb=" C2 BCLAM1001 " -0.080 1.50e-02 4.44e+03 pdb=" C3 BCLAM1001 " -0.045 1.50e-02 4.44e+03 pdb=" C4 BCLAM1001 " -0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAM1001 " 0.059 1.50e-02 4.44e+03 ... (remaining 3925 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 92 2.63 - 3.19: 18591 3.19 - 3.76: 36999 3.76 - 4.33: 53354 4.33 - 4.90: 84548 Nonbonded interactions: 193584 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 408 " model vdw 2.058 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 408 " model vdw 2.107 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 408 " model vdw 2.237 2.340 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE M 408 " model vdw 2.269 2.340 nonbonded pdb=" NE2 HIS L 230 " pdb="FE FE M 408 " model vdw 2.339 2.340 ... (remaining 193579 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 'AA' and resid 4 through 46) selection = (chain 'AL' and resid 4 through 46) selection = (chain 'AN' and resid 4 through 46) } ncs_group { reference = (chain 'AB' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AC' and resid 1 through 55) selection = (chain 'AD' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AE' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AF' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AG' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AH' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AI' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AJ' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AK' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'AM' and (resid 1 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'BA' and resid 11 through 48) selection = (chain 'BB' and resid 11 through 48) selection = (chain 'BC' and resid 11 through 48) selection = (chain 'BD' and resid 11 through 48) selection = (chain 'BE' and resid 11 through 48) selection = (chain 'BF' and resid 11 through 48) selection = (chain 'BG' and resid 11 through 48) selection = (chain 'BH' and resid 11 through 48) selection = (chain 'BI' and resid 11 through 48) selection = (chain 'BJ' and resid 11 through 48) selection = (chain 'BK' and resid 11 through 48) selection = (chain 'BL' and resid 11 through 48) selection = (chain 'BM' and resid 11 through 48) selection = (chain 'BN' and resid 11 through 48) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.600 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 60.620 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.070 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 23344 Z= 0.282 Angle : 0.984 14.469 32052 Z= 0.471 Chirality : 0.050 0.218 3156 Planarity : 0.009 0.138 3928 Dihedral : 16.605 179.766 8408 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.21 % Allowed : 0.95 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 2225 helix: 1.03 (0.11), residues: 1420 sheet: 0.96 (0.96), residues: 22 loop : 0.39 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPBK 47 HIS 0.013 0.002 HIS L 153 PHE 0.029 0.003 PHEAJ 11 TYR 0.040 0.005 TYRBL 8 ARG 0.024 0.004 ARGAD 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 470 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: AE 15 ARG cc_start: 0.7176 (ttm-80) cc_final: 0.6254 (ttt-90) REVERT: AE 52 ASN cc_start: 0.7979 (m-40) cc_final: 0.7707 (m110) REVERT: AI 9 MET cc_start: 0.7656 (mtp) cc_final: 0.7445 (mtp) REVERT: AJ 54 VAL cc_start: 0.6622 (t) cc_final: 0.6396 (m) REVERT: BG 42 TYR cc_start: 0.8539 (t80) cc_final: 0.8326 (t80) REVERT: H 60 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7699 (mtmm) REVERT: M 292 ASP cc_start: 0.7867 (p0) cc_final: 0.7547 (p0) REVERT: X 29 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7174 (tttp) outliers start: 4 outliers final: 3 residues processed: 473 average time/residue: 1.2947 time to fit residues: 699.4570 Evaluate side-chains 353 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 3.9990 chunk 162 optimal weight: 0.0570 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 109 optimal weight: 0.0370 chunk 87 optimal weight: 7.9990 chunk 168 optimal weight: 0.3980 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 20 GLN AG 20 GLN AH 20 GLN AI 20 GLN AJ 20 GLN AL 20 GLN BA 15 GLN BC 17 GLN BE 15 GLN L 62 GLN X 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23344 Z= 0.153 Angle : 0.634 12.516 32052 Z= 0.260 Chirality : 0.037 0.153 3156 Planarity : 0.003 0.040 3928 Dihedral : 16.021 179.927 4416 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.85 % Allowed : 8.49 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 3.52 (0.17), residues: 2225 helix: 2.81 (0.12), residues: 1503 sheet: -0.51 (1.02), residues: 24 loop : 1.52 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPBK 47 HIS 0.006 0.001 HIS L 153 PHE 0.020 0.002 PHEAJ 17 TYR 0.012 0.001 TYRAM 41 ARG 0.003 0.001 ARGAF 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 378 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: AB 2 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7893 (t) REVERT: AF 30 MET cc_start: 0.7675 (mmm) cc_final: 0.7445 (mmp) REVERT: AG 15 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7176 (mtp85) REVERT: AJ 54 VAL cc_start: 0.6578 (t) cc_final: 0.6357 (m) REVERT: AL 9 MET cc_start: 0.7496 (mmm) cc_final: 0.6871 (mpp) REVERT: AL 10 ILE cc_start: 0.7875 (mm) cc_final: 0.7457 (tt) REVERT: AM 1 MET cc_start: 0.4701 (tpt) cc_final: 0.4191 (tpt) REVERT: BC 24 MET cc_start: 0.8491 (mmm) cc_final: 0.8207 (mmm) REVERT: BE 17 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: BK 17 GLN cc_start: 0.6815 (mt0) cc_final: 0.6612 (mt0) REVERT: BM 28 TRP cc_start: 0.6718 (m100) cc_final: 0.5854 (m-90) REVERT: H 60 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7571 (mtmm) REVERT: M 292 ASP cc_start: 0.7862 (p0) cc_final: 0.7556 (p0) outliers start: 35 outliers final: 9 residues processed: 389 average time/residue: 1.1960 time to fit residues: 536.6422 Evaluate side-chains 348 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 337 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 37 SER Chi-restraints excluded: chain AB residue 2 SER Chi-restraints excluded: chain AG residue 2 SER Chi-restraints excluded: chain AG residue 40 SER Chi-restraints excluded: chain BE residue 17 GLN Chi-restraints excluded: chain BI residue 19 LEU Chi-restraints excluded: chain BK residue 12 THR Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain M residue 303 MET Chi-restraints excluded: chain X residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4688 > 50: distance: 123 - 129: 13.789 distance: 129 - 130: 10.086 distance: 130 - 131: 8.537 distance: 131 - 132: 21.657 distance: 131 - 133: 14.798 distance: 133 - 134: 11.549 distance: 134 - 135: 8.494 distance: 134 - 137: 11.871 distance: 135 - 136: 13.741 distance: 135 - 138: 8.136 distance: 138 - 139: 5.683 distance: 139 - 140: 9.898 distance: 139 - 142: 10.642 distance: 140 - 141: 23.800 distance: 140 - 152: 14.460 distance: 142 - 143: 9.897 distance: 143 - 144: 4.447 distance: 143 - 145: 9.412 distance: 144 - 146: 8.597 distance: 145 - 147: 11.689 distance: 145 - 148: 4.489 distance: 146 - 147: 10.815 distance: 147 - 149: 12.024 distance: 148 - 150: 4.671 distance: 149 - 151: 3.586 distance: 150 - 151: 5.248 distance: 152 - 153: 5.683 distance: 153 - 154: 11.149 distance: 154 - 155: 27.183 distance: 154 - 156: 30.260 distance: 156 - 157: 31.536 distance: 157 - 158: 25.237 distance: 157 - 160: 20.086 distance: 158 - 159: 14.835 distance: 158 - 168: 34.499 distance: 160 - 161: 10.068 distance: 161 - 162: 20.655 distance: 161 - 163: 10.582 distance: 162 - 164: 4.684 distance: 163 - 165: 6.873 distance: 164 - 166: 18.389 distance: 165 - 166: 13.960 distance: 166 - 167: 3.495 distance: 168 - 169: 21.330 distance: 169 - 170: 26.385 distance: 169 - 172: 20.441 distance: 170 - 171: 33.580 distance: 170 - 173: 13.751 distance: 173 - 174: 11.701 distance: 174 - 175: 35.002 distance: 174 - 177: 39.593 distance: 175 - 176: 31.818 distance: 175 - 184: 26.530 distance: 177 - 178: 13.023 distance: 178 - 179: 11.970 distance: 178 - 180: 43.777 distance: 179 - 181: 13.674 distance: 180 - 182: 10.155 distance: 181 - 183: 25.904 distance: 182 - 183: 20.220 distance: 184 - 185: 10.421 distance: 184 - 190: 30.767 distance: 185 - 186: 15.031 distance: 185 - 188: 22.446 distance: 186 - 187: 27.812 distance: 186 - 191: 14.609 distance: 188 - 189: 41.138 distance: 189 - 190: 20.326 distance: 191 - 192: 19.588 distance: 192 - 193: 6.319 distance: 192 - 195: 4.870 distance: 193 - 194: 17.443 distance: 193 - 203: 32.014 distance: 195 - 196: 16.396 distance: 196 - 197: 11.748 distance: 196 - 198: 35.898 distance: 197 - 199: 3.471 distance: 198 - 200: 13.654 distance: 199 - 201: 23.150 distance: 200 - 201: 27.827 distance: 201 - 202: 5.792 distance: 203 - 204: 34.283 distance: 204 - 205: 14.396 distance: 205 - 206: 20.830 distance: 205 - 207: 28.376