Starting phenix.real_space_refine (version: dev) on Fri Feb 24 09:36:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_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_13441/02_2023/7pil_13441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_2023/7pil_13441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pil_13441/02_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 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-4877/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: 12.73, per 1000 atoms: 0.57 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: 10.05 Conformation dependent library (CDL) restraints added in 2.7 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: 1.35 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: 5.92 Time building geometry restraints manager: 10.71 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: 12025 35.95 - 71.91: 240 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: 2120 0.044 - 0.087: 774 0.087 - 0.131: 204 0.131 - 0.174: 54 0.174 - 0.218: 4 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=" C2C BPH L 301 " pdb=" C1C BPH L 301 " pdb=" C3C BPH L 301 " pdb=" CMC BPH L 301 " both_signs ideal model delta sigma weight residual False -2.81 -2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C3C BPH L 301 " pdb=" C2C BPH L 301 " pdb=" C4C BPH L 301 " pdb=" CAC BPH L 301 " both_signs ideal model delta sigma weight residual False 2.83 2.65 0.18 2.00e-01 2.50e+01 8.31e-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 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. 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 28.610 Check model and map are aligned: 0.410 Process input model: 56.910 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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= 0.268 Angle : 0.963 14.469 32052 Z= 0.467 Chirality : 0.049 0.218 3156 Planarity : 0.009 0.138 3928 Dihedral : 16.359 179.766 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 : 3.419 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 473 average time/residue: 1.3645 time to fit residues: 736.8273 Evaluate side-chains 352 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 349 time to evaluate : 2.489 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.9274 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.1831 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= 0.154 Angle : 0.637 12.289 32052 Z= 0.265 Chirality : 0.037 0.161 3156 Planarity : 0.003 0.041 3928 Dihedral : 15.833 179.912 4066 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer Outliers : 1.74 % 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: 3.38 (0.17), residues: 2225 helix: 2.68 (0.12), residues: 1490 sheet: 1.96 (1.52), residues: 12 loop : 1.46 (0.25), residues: 723 *********************** 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 401 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 368 time to evaluate : 2.202 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 380 average time/residue: 1.2375 time to fit residues: 548.8146 Evaluate side-chains 338 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 330 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.5446 time to fit residues: 5.7401 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 174 optimal weight: 0.0870 chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 23344 Z= 0.168 Angle : 0.633 12.940 32052 Z= 0.259 Chirality : 0.038 0.134 3156 Planarity : 0.003 0.039 3928 Dihedral : 15.769 179.934 4066 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.64 % 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: 3.57 (0.17), residues: 2225 helix: 2.88 (0.12), residues: 1490 sheet: -0.22 (1.02), residues: 24 loop : 1.47 (0.25), residues: 711 *********************** 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 405 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 355 time to evaluate : 2.397 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 19 residues processed: 373 average time/residue: 1.2236 time to fit residues: 527.5127 Evaluate side-chains 344 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 325 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 7 residues processed: 12 average time/residue: 0.4550 time to fit residues: 10.7140 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.2646 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= 0.192 Angle : 0.658 13.570 32052 Z= 0.267 Chirality : 0.038 0.134 3156 Planarity : 0.004 0.039 3928 Dihedral : 15.843 179.905 4066 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 3.40 (0.17), residues: 2225 helix: 2.75 (0.12), residues: 1488 sheet: 2.41 (1.44), residues: 12 loop : 1.32 (0.24), residues: 725 *********************** 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 394 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 346 time to evaluate : 2.432 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 366 average time/residue: 1.2452 time to fit residues: 525.2521 Evaluate side-chains 348 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 326 time to evaluate : 2.441 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.4696 time to fit residues: 10.0467 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23344 Z= 0.222 Angle : 0.688 14.455 32052 Z= 0.279 Chirality : 0.039 0.142 3156 Planarity : 0.004 0.037 3928 Dihedral : 15.839 179.866 4066 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.36 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: 3.16 (0.17), residues: 2225 helix: 2.63 (0.12), residues: 1487 sheet: -0.24 (1.02), residues: 24 loop : 1.16 (0.24), residues: 714 *********************** 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 383 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 334 time to evaluate : 2.250 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 350 average time/residue: 1.3104 time to fit residues: 527.5036 Evaluate side-chains 347 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 321 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 12 residues processed: 14 average time/residue: 0.5291 time to fit residues: 12.8950 ------------------------------------------------------------------------------- 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: 7.9990 chunk 187 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 BK 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 23344 Z= 0.362 Angle : 0.839 16.978 32052 Z= 0.338 Chirality : 0.045 0.227 3156 Planarity : 0.005 0.059 3928 Dihedral : 16.747 179.724 4066 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 3.27 % 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: 2.48 (0.17), residues: 2225 helix: 2.12 (0.12), residues: 1494 sheet: 0.87 (1.13), residues: 19 loop : 0.78 (0.24), residues: 712 *********************** 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 395 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 333 time to evaluate : 2.408 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 32 residues processed: 360 average time/residue: 1.3098 time to fit residues: 541.5357 Evaluate side-chains 358 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 326 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 19 residues processed: 13 average time/residue: 0.6058 time to fit residues: 13.2010 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 129 optimal weight: 0.0670 chunk 126 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23344 Z= 0.182 Angle : 0.658 14.294 32052 Z= 0.264 Chirality : 0.038 0.150 3156 Planarity : 0.004 0.038 3928 Dihedral : 15.744 179.914 4066 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer Outliers : 2.11 % 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: 2.99 (0.17), residues: 2225 helix: 2.55 (0.12), residues: 1486 sheet: -0.12 (1.02), residues: 24 loop : 0.94 (0.24), residues: 715 *********************** 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: 40 poor density : 345 time to evaluate : 2.619 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 363 average time/residue: 1.2857 time to fit residues: 538.5288 Evaluate side-chains 357 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 335 time to evaluate : 2.564 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 9 average time/residue: 0.3786 time to fit residues: 8.1958 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 162 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8429 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23344 Z= 0.175 Angle : 0.642 13.763 32052 Z= 0.257 Chirality : 0.037 0.139 3156 Planarity : 0.003 0.037 3928 Dihedral : 15.380 179.941 4066 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 3.13 (0.17), residues: 2225 helix: 2.66 (0.12), residues: 1486 sheet: -0.08 (1.03), residues: 24 loop : 1.01 (0.24), residues: 715 *********************** 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: 35 poor density : 337 time to evaluate : 2.424 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 353 average time/residue: 1.3534 time to fit residues: 548.8819 Evaluate side-chains 351 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 331 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.4744 time to fit residues: 6.9643 ------------------------------------------------------------------------------- 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: 2.9990 chunk 181 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 23344 Z= 0.249 Angle : 0.729 14.957 32052 Z= 0.293 Chirality : 0.040 0.175 3156 Planarity : 0.004 0.038 3928 Dihedral : 15.873 179.854 4066 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 2.00 % 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: 2.78 (0.17), residues: 2225 helix: 2.40 (0.12), residues: 1492 sheet: -0.16 (1.02), residues: 24 loop : 0.81 (0.24), residues: 709 *********************** 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 371 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 333 time to evaluate : 2.603 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 353 average time/residue: 1.3115 time to fit residues: 534.9110 Evaluate side-chains 355 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 330 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.3384 time to fit residues: 8.0362 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 0.0050 chunk 104 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 overall best weight: 0.5294 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23344 Z= 0.153 Angle : 0.620 13.217 32052 Z= 0.249 Chirality : 0.037 0.140 3156 Planarity : 0.003 0.038 3928 Dihedral : 15.209 179.974 4066 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer Outliers : 1.16 % 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: 3.22 (0.17), residues: 2225 helix: 2.75 (0.12), residues: 1485 sheet: 0.06 (1.05), residues: 24 loop : 0.96 (0.24), residues: 716 ********************** 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 354 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 332 time to evaluate : 2.419 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 346 average time/residue: 1.3139 time to fit residues: 523.8787 Evaluate side-chains 342 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 326 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.3043 time to fit residues: 5.1246 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114060 restraints weight = 22635.461| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.99 r_work: 0.3150 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3069 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= 0.280 Angle : 0.760 15.336 32052 Z= 0.307 Chirality : 0.042 0.185 3156 Planarity : 0.004 0.044 3928 Dihedral : 15.971 179.803 4066 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.32 % 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: 2.71 (0.17), residues: 2225 helix: 2.36 (0.12), residues: 1491 sheet: -0.17 (1.03), residues: 24 loop : 0.76 (0.24), residues: 710 =============================================================================== Job complete usr+sys time: 8933.03 seconds wall clock time: 158 minutes 55.92 seconds (9535.92 seconds total)