Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 09:44:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_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_13441/04_2023/7pil_13441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/04_2023/7pil_13441_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-1.21rc1-4938/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: 11.87, per 1000 atoms: 0.53 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: 9.82 Conformation dependent library (CDL) restraints added in 2.8 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: 1.37 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: 6.60 Time building geometry restraints manager: 10.37 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: 12026 35.95 - 71.91: 239 71.91 - 107.86: 36 107.86 - 143.81: 11 143.81 - 179.77: 9 Dihedral angle restraints: 12321 sinusoidal: 5696 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 12318 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: 7.070 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: 28.210 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 56.120 Find NCS groups from input model: 1.170 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: 0.000 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.660 ------------------------------------------------------------------------------- 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 : 16.344 179.766 8063 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 % 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 *********************** 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 : 2.451 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 473 average time/residue: 1.3212 time to fit residues: 713.6711 Evaluate side-chains 352 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 349 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.8170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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: 0.8187 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23344 Z= 0.152 Angle : 0.630 12.514 32052 Z= 0.260 Chirality : 0.037 0.163 3156 Planarity : 0.003 0.041 3928 Dihedral : 15.732 179.923 4066 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 1.85 % 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: 3.50 (0.17), residues: 2225 helix: 2.76 (0.12), residues: 1505 sheet: 1.94 (1.51), residues: 12 loop : 1.50 (0.25), residues: 708 *********************** 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 411 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 376 time to evaluate : 2.451 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 388 average time/residue: 1.2745 time to fit residues: 573.2646 Evaluate side-chains 341 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 332 time to evaluate : 2.474 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.4275 time to fit residues: 6.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 20 GLN ** AE 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 20 GLN AJ 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 23344 Z= 0.231 Angle : 0.712 13.512 32052 Z= 0.292 Chirality : 0.040 0.139 3156 Planarity : 0.004 0.040 3928 Dihedral : 16.344 179.854 4066 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 2.58 % 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: 3.25 (0.17), residues: 2225 helix: 2.64 (0.12), residues: 1489 sheet: -0.38 (1.02), residues: 24 loop : 1.34 (0.25), residues: 712 *********************** REFINEMENT MACRO_CYCLE 3 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 398 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 349 time to evaluate : 2.457 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 369 average time/residue: 1.2452 time to fit residues: 532.3561 Evaluate side-chains 348 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 324 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 13 average time/residue: 0.5179 time to fit residues: 11.8306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 20 GLN AJ 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23344 Z= 0.178 Angle : 0.636 13.626 32052 Z= 0.258 Chirality : 0.038 0.134 3156 Planarity : 0.003 0.041 3928 Dihedral : 15.763 179.928 4066 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 2.80 % 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: 3.39 (0.17), residues: 2225 helix: 2.77 (0.12), residues: 1487 sheet: 2.39 (1.45), residues: 12 loop : 1.25 (0.24), residues: 726 *********************** REFINEMENT MACRO_CYCLE 4 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 396 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 343 time to evaluate : 2.352 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 362 average time/residue: 1.2515 time to fit residues: 523.4136 Evaluate side-chains 350 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 328 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.3586 time to fit residues: 8.8720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 177 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AE 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 20 GLN AJ 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 23344 Z= 0.308 Angle : 0.785 15.928 32052 Z= 0.317 Chirality : 0.043 0.161 3156 Planarity : 0.005 0.049 3928 Dihedral : 16.535 179.733 4066 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 2.80 % 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: 2.75 (0.17), residues: 2225 helix: 2.31 (0.12), residues: 1494 sheet: 2.35 (1.44), residues: 12 loop : 0.91 (0.24), residues: 719 *********************** REFINEMENT MACRO_CYCLE 5 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 393 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 340 time to evaluate : 2.310 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 362 average time/residue: 1.2762 time to fit residues: 533.3579 Evaluate side-chains 352 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 326 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 11 average time/residue: 0.6874 time to fit residues: 12.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AE 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 23344 Z= 0.293 Angle : 0.767 16.042 32052 Z= 0.309 Chirality : 0.042 0.197 3156 Planarity : 0.004 0.050 3928 Dihedral : 16.345 179.811 4066 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 3.01 % 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: 2.56 (0.17), residues: 2225 helix: 2.22 (0.12), residues: 1492 sheet: -0.20 (1.01), residues: 24 loop : 0.75 (0.24), residues: 709 *********************** REFINEMENT MACRO_CYCLE 6 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 385 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 328 time to evaluate : 2.298 Fit side-chains outliers start: 57 outliers final: 31 residues processed: 352 average time/residue: 1.2626 time to fit residues: 513.6157 Evaluate side-chains 354 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 323 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 11 average time/residue: 0.5471 time to fit residues: 10.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AL 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23344 Z= 0.263 Angle : 0.747 15.637 32052 Z= 0.298 Chirality : 0.041 0.180 3156 Planarity : 0.004 0.045 3928 Dihedral : 16.141 179.862 4066 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 2.53 % 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: 2.64 (0.17), residues: 2225 helix: 2.28 (0.12), residues: 1488 sheet: -0.21 (1.01), residues: 24 loop : 0.82 (0.24), residues: 713 *********************** REFINEMENT MACRO_CYCLE 7 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 385 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 337 time to evaluate : 2.440 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 360 average time/residue: 1.3312 time to fit residues: 553.7863 Evaluate side-chains 356 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 2.378 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.6019 time to fit residues: 10.8630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 162 optimal weight: 0.0770 chunk 188 optimal weight: 0.5980 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AL 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 23344 Z= 0.277 Angle : 0.766 15.837 32052 Z= 0.305 Chirality : 0.042 0.188 3156 Planarity : 0.004 0.047 3928 Dihedral : 16.231 179.884 4066 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 2.22 % 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: 2.50 (0.17), residues: 2225 helix: 2.19 (0.12), residues: 1492 sheet: -0.19 (1.01), residues: 24 loop : 0.70 (0.24), residues: 709 *********************** REFINEMENT MACRO_CYCLE 8 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 372 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 330 time to evaluate : 2.150 Fit side-chains outliers start: 42 outliers final: 26 residues processed: 351 average time/residue: 1.2677 time to fit residues: 511.9806 Evaluate side-chains 355 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 329 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.4305 time to fit residues: 7.8674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 192 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AL 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23344 Z= 0.172 Angle : 0.654 13.948 32052 Z= 0.261 Chirality : 0.037 0.147 3156 Planarity : 0.004 0.038 3928 Dihedral : 15.517 179.991 4066 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 1.85 % 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: 3.03 (0.17), residues: 2225 helix: 2.61 (0.12), residues: 1485 sheet: -0.06 (1.04), residues: 24 loop : 0.90 (0.24), residues: 716 *********************** REFINEMENT MACRO_CYCLE 9 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 379 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 344 time to evaluate : 2.309 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 364 average time/residue: 1.3002 time to fit residues: 547.9577 Evaluate side-chains 350 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 330 time to evaluate : 2.414 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.3162 time to fit residues: 4.9592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN BK 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 23344 Z= 0.256 Angle : 0.744 15.218 32052 Z= 0.298 Chirality : 0.041 0.177 3156 Planarity : 0.004 0.041 3928 Dihedral : 15.931 179.887 4066 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 1.53 % 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: 2.74 (0.17), residues: 2225 helix: 2.37 (0.12), residues: 1485 sheet: 2.51 (1.44), residues: 12 loop : 0.75 (0.23), residues: 728 ********************** REFINEMENT MACRO_CYCLE 10 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 360 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 2.137 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 350 average time/residue: 1.3131 time to fit residues: 528.9148 Evaluate side-chains 344 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 324 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.6078 time to fit residues: 5.2877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN AL 20 GLN ** AM 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112910 restraints weight = 22440.504| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.98 r_work: 0.3120 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23344 Z= 0.264 Angle : 0.757 15.398 32052 Z= 0.303 Chirality : 0.041 0.180 3156 Planarity : 0.004 0.043 3928 Dihedral : 16.031 179.917 4066 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.48 % 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: 2.57 (0.17), residues: 2225 helix: 2.26 (0.12), residues: 1491 sheet: -0.13 (1.02), residues: 24 loop : 0.67 (0.23), residues: 710 =============================================================================== Job complete usr+sys time: 8846.55 seconds wall clock time: 157 minutes 53.17 seconds (9473.17 seconds total)