Starting phenix.real_space_refine on Sat Feb 17 02:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyq_32211/02_2024/7vyq_32211_trim_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 P 12 5.49 5 S 28 5.16 5 Cl 4 4.86 5 C 5520 2.51 5 N 1420 2.21 5 O 1756 1.98 5 H 8340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G ASP 108": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "B" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "F" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "G" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.05, per 1000 atoms: 0.47 Number of scatterers: 17080 At special positions: 0 Unit cell: (94.581, 87.885, 97.092, 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) Cl 4 17.00 S 28 16.00 P 12 15.00 O 1756 8.00 N 1420 7.00 C 5520 6.00 H 8340 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 36.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.603A pdb=" N GLU A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 146 through 162 removed outlier: 4.018A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 185 through 204 removed outlier: 3.558A pdb=" N LYS A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.602A pdb=" N LYS A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'B' and resid 10 through 12 No H-bonds generated for 'chain 'B' and resid 10 through 12' Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.607A pdb=" N GLU B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 146 through 162 removed outlier: 3.977A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 185 through 204 removed outlier: 3.558A pdb=" N LYS B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.590A pdb=" N LYS B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 235 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'F' and resid 10 through 12 No H-bonds generated for 'chain 'F' and resid 10 through 12' Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 95 through 103 removed outlier: 3.665A pdb=" N GLU F 99 " --> pdb=" O PRO F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 108 No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 136 through 143 Processing helix chain 'F' and resid 146 through 162 removed outlier: 4.102A pdb=" N LYS F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS F 161 " --> pdb=" O LYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 185 through 204 removed outlier: 3.893A pdb=" N LYS F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 203 " --> pdb=" O LYS F 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 204 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 236 removed outlier: 3.593A pdb=" N LYS F 234 " --> pdb=" O ASP F 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP F 235 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 95 through 103 removed outlier: 3.604A pdb=" N GLU G 99 " --> pdb=" O PRO G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 108 No H-bonds generated for 'chain 'G' and resid 105 through 108' Processing helix chain 'G' and resid 136 through 143 Processing helix chain 'G' and resid 146 through 162 removed outlier: 3.501A pdb=" N ASN G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 185 through 204 removed outlier: 3.560A pdb=" N LYS G 199 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 204 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.590A pdb=" N LYS G 234 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP G 235 " --> pdb=" O MET G 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 251 through 258 Processing sheet with id= A, first strand: chain 'A' and resid 114 through 116 removed outlier: 6.106A pdb=" N ASP A 60 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 39 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A 62 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A 86 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR A 65 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR A 88 " --> pdb=" O TYR A 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 169 Processing sheet with id= C, first strand: chain 'B' and resid 114 through 116 removed outlier: 6.133A pdb=" N ASP B 60 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 39 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA B 62 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS B 86 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 65 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR B 88 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= E, first strand: chain 'F' and resid 114 through 116 removed outlier: 6.113A pdb=" N ASP F 60 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL F 39 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA F 62 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS F 86 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR F 65 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR F 88 " --> pdb=" O TYR F 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 167 through 169 Processing sheet with id= G, first strand: chain 'G' and resid 114 through 116 removed outlier: 6.120A pdb=" N ASP G 60 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL G 39 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA G 62 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS G 86 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR G 65 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR G 88 " --> pdb=" O TYR G 65 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 167 through 169 207 hydrogen bonds defined for protein. 609 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: 6.05 Time building geometry restraints manager: 14.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8320 1.03 - 1.23: 44 1.23 - 1.42: 3754 1.42 - 1.62: 5134 1.62 - 1.82: 40 Bond restraints: 17292 Sorted by residual: bond pdb=" O2B NAP G 301 " pdb=" P2B NAP G 301 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" O2B NAP A 301 " pdb=" P2B NAP A 301 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" O2B NAP F 301 " pdb=" P2B NAP F 301 " ideal model delta sigma weight residual 1.736 1.602 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O2B NAP B 301 " pdb=" P2B NAP B 301 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.46e+01 bond pdb=" O5D NAP B 301 " pdb=" PN NAP B 301 " ideal model delta sigma weight residual 1.649 1.587 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 17287 not shown) Histogram of bond angle deviations from ideal: 95.59 - 103.27: 85 103.27 - 110.95: 18656 110.95 - 118.63: 4996 118.63 - 126.31: 7209 126.31 - 133.99: 250 Bond angle restraints: 31196 Sorted by residual: angle pdb=" O2B NAP F 301 " pdb=" P2B NAP F 301 " pdb=" O2X NAP F 301 " ideal model delta sigma weight residual 100.14 113.36 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O2B NAP B 301 " pdb=" P2B NAP B 301 " pdb=" O2X NAP B 301 " ideal model delta sigma weight residual 100.14 113.25 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O2B NAP G 301 " pdb=" P2B NAP G 301 " pdb=" O2X NAP G 301 " ideal model delta sigma weight residual 100.14 112.17 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O2B NAP A 301 " pdb=" P2B NAP A 301 " pdb=" O2X NAP A 301 " ideal model delta sigma weight residual 100.14 112.15 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C3D NAP F 301 " pdb=" C2D NAP F 301 " pdb=" O2D NAP F 301 " ideal model delta sigma weight residual 116.01 104.56 11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 31191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7222 17.88 - 35.76: 731 35.76 - 53.65: 315 53.65 - 71.53: 105 71.53 - 89.41: 19 Dihedral angle restraints: 8392 sinusoidal: 4608 harmonic: 3784 Sorted by residual: dihedral pdb=" CA ASP F 71 " pdb=" CB ASP F 71 " pdb=" CG ASP F 71 " pdb=" OD1 ASP F 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.26 55.26 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP B 71 " pdb=" CB ASP B 71 " pdb=" CG ASP B 71 " pdb=" OD1 ASP B 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.23 55.23 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP A 71 " pdb=" CB ASP A 71 " pdb=" CG ASP A 71 " pdb=" OD1 ASP A 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.22 55.22 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 8389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 918 0.037 - 0.073: 319 0.073 - 0.110: 91 0.110 - 0.147: 26 0.147 - 0.183: 6 Chirality restraints: 1360 Sorted by residual: chirality pdb=" C2D NAP F 301 " pdb=" C1D NAP F 301 " pdb=" C3D NAP F 301 " pdb=" O2D NAP F 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.73 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" C4D NAP A 301 " pdb=" C3D NAP A 301 " pdb=" C5D NAP A 301 " pdb=" O4D NAP A 301 " both_signs ideal model delta sigma weight residual False -2.58 -2.41 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" C4D NAP G 301 " pdb=" C3D NAP G 301 " pdb=" C5D NAP G 301 " pdb=" O4D NAP G 301 " both_signs ideal model delta sigma weight residual False -2.58 -2.41 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 1357 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 301 " -0.222 2.00e-02 2.50e+03 1.62e-01 5.28e+02 pdb=" C2N NAP A 301 " 0.287 2.00e-02 2.50e+03 pdb=" C3N NAP A 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAP A 301 " -0.243 2.00e-02 2.50e+03 pdb=" C5N NAP A 301 " 0.091 2.00e-02 2.50e+03 pdb=" C6N NAP A 301 " 0.092 2.00e-02 2.50e+03 pdb=" C7N NAP A 301 " -0.050 2.00e-02 2.50e+03 pdb=" N1N NAP A 301 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAP B 301 " -0.220 2.00e-02 2.50e+03 1.61e-01 5.19e+02 pdb=" C2N NAP B 301 " 0.285 2.00e-02 2.50e+03 pdb=" C3N NAP B 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAP B 301 " -0.239 2.00e-02 2.50e+03 pdb=" C5N NAP B 301 " 0.087 2.00e-02 2.50e+03 pdb=" C6N NAP B 301 " 0.094 2.00e-02 2.50e+03 pdb=" C7N NAP B 301 " -0.050 2.00e-02 2.50e+03 pdb=" N1N NAP B 301 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAP G 301 " 0.218 2.00e-02 2.50e+03 1.60e-01 5.12e+02 pdb=" C2N NAP G 301 " -0.287 2.00e-02 2.50e+03 pdb=" C3N NAP G 301 " -0.009 2.00e-02 2.50e+03 pdb=" C4N NAP G 301 " 0.236 2.00e-02 2.50e+03 pdb=" C5N NAP G 301 " -0.090 2.00e-02 2.50e+03 pdb=" C6N NAP G 301 " -0.085 2.00e-02 2.50e+03 pdb=" C7N NAP G 301 " 0.053 2.00e-02 2.50e+03 pdb=" N1N NAP G 301 " -0.036 2.00e-02 2.50e+03 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1555 2.22 - 2.82: 37045 2.82 - 3.41: 46679 3.41 - 4.01: 66842 4.01 - 4.60: 102061 Nonbonded interactions: 254182 Sorted by model distance: nonbonded pdb=" OD1 ASN B 146 " pdb=" HE1 TRP F 137 " model vdw 1.625 1.850 nonbonded pdb=" OD1 ASN A 146 " pdb=" HE1 TRP G 137 " model vdw 1.629 1.850 nonbonded pdb="HE22 GLN G 125 " pdb=" OG SER G 136 " model vdw 1.678 1.850 nonbonded pdb="HE22 GLN F 125 " pdb=" OG SER F 136 " model vdw 1.684 1.850 nonbonded pdb="HD22 ASN F 133 " pdb=" OD2 ASP F 135 " model vdw 1.686 1.850 ... (remaining 254177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' } 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: 1.070 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: 0.260 Extract box with map and model: 4.550 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 57.800 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 0.138 8952 Z= 0.323 Angle : 0.776 13.215 12212 Z= 0.387 Chirality : 0.042 0.183 1360 Planarity : 0.009 0.162 1528 Dihedral : 19.426 89.408 3376 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 22.71 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.84 (0.27), residues: 1112 helix: -0.91 (0.25), residues: 436 sheet: -2.79 (0.39), residues: 180 loop : -0.64 (0.31), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 64 HIS 0.002 0.000 HIS A 196 PHE 0.005 0.000 PHE B 208 TYR 0.004 0.000 TYR F 65 ARG 0.001 0.000 ARG F 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.374 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.4409 time to fit residues: 43.8981 Evaluate side-chains 64 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.250 Angle : 0.477 4.217 12212 Z= 0.239 Chirality : 0.043 0.129 1360 Planarity : 0.004 0.049 1528 Dihedral : 12.014 75.810 1480 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.66 % Allowed : 21.07 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.42 (0.27), residues: 1112 helix: -0.40 (0.26), residues: 444 sheet: -1.55 (0.45), residues: 156 loop : -1.09 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 64 HIS 0.004 0.001 HIS A 196 PHE 0.011 0.001 PHE B 208 TYR 0.008 0.001 TYR F 149 ARG 0.000 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.4499 time to fit residues: 47.6982 Evaluate side-chains 70 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.0000 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8952 Z= 0.147 Angle : 0.437 4.208 12212 Z= 0.215 Chirality : 0.041 0.124 1360 Planarity : 0.003 0.050 1528 Dihedral : 10.704 74.677 1480 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.44 % Allowed : 20.63 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.07 (0.27), residues: 1112 helix: 0.00 (0.27), residues: 444 sheet: -1.39 (0.45), residues: 148 loop : -1.03 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 64 HIS 0.003 0.001 HIS F 196 PHE 0.008 0.001 PHE G 208 TYR 0.007 0.001 TYR F 149 ARG 0.000 0.000 ARG F 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.4739 time to fit residues: 48.1767 Evaluate side-chains 67 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8952 Z= 0.173 Angle : 0.444 4.180 12212 Z= 0.219 Chirality : 0.041 0.124 1360 Planarity : 0.003 0.049 1528 Dihedral : 10.308 75.054 1480 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.87 % Allowed : 20.63 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.97 (0.27), residues: 1112 helix: 0.15 (0.27), residues: 444 sheet: -1.38 (0.45), residues: 148 loop : -1.02 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 64 HIS 0.003 0.001 HIS A 196 PHE 0.008 0.001 PHE B 208 TYR 0.007 0.001 TYR F 149 ARG 0.000 0.000 ARG G 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.5032 time to fit residues: 51.9846 Evaluate side-chains 75 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8952 Z= 0.312 Angle : 0.500 4.094 12212 Z= 0.250 Chirality : 0.044 0.125 1360 Planarity : 0.004 0.049 1528 Dihedral : 10.961 71.835 1480 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.20 % Allowed : 20.31 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.23 (0.27), residues: 1112 helix: -0.01 (0.27), residues: 444 sheet: -1.65 (0.42), residues: 156 loop : -1.16 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 64 HIS 0.003 0.001 HIS A 196 PHE 0.012 0.001 PHE B 208 TYR 0.007 0.001 TYR A 149 ARG 0.001 0.000 ARG G 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 73 average time/residue: 0.4942 time to fit residues: 50.0787 Evaluate side-chains 73 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.230 Angle : 0.467 4.078 12212 Z= 0.232 Chirality : 0.042 0.124 1360 Planarity : 0.003 0.049 1528 Dihedral : 10.682 71.760 1480 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.20 % Allowed : 20.31 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.17 (0.27), residues: 1112 helix: 0.06 (0.27), residues: 444 sheet: -1.69 (0.42), residues: 156 loop : -1.14 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 64 HIS 0.003 0.001 HIS A 196 PHE 0.010 0.001 PHE B 208 TYR 0.007 0.001 TYR A 149 ARG 0.000 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.4811 time to fit residues: 49.5883 Evaluate side-chains 73 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8952 Z= 0.221 Angle : 0.466 4.085 12212 Z= 0.232 Chirality : 0.042 0.125 1360 Planarity : 0.003 0.048 1528 Dihedral : 10.519 72.088 1480 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.31 % Allowed : 20.52 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.11 (0.27), residues: 1112 helix: 0.20 (0.27), residues: 440 sheet: -1.60 (0.43), residues: 148 loop : -1.22 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 64 HIS 0.003 0.001 HIS A 196 PHE 0.010 0.001 PHE B 208 TYR 0.007 0.001 TYR A 149 ARG 0.000 0.000 ARG F 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.5020 time to fit residues: 50.7327 Evaluate side-chains 73 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8952 Z= 0.332 Angle : 0.510 4.181 12212 Z= 0.256 Chirality : 0.044 0.124 1360 Planarity : 0.004 0.048 1528 Dihedral : 11.100 68.229 1480 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.75 % Allowed : 20.41 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.34 (0.26), residues: 1112 helix: -0.03 (0.26), residues: 444 sheet: -1.84 (0.40), residues: 156 loop : -1.25 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 123 HIS 0.004 0.001 HIS G 196 PHE 0.012 0.001 PHE B 208 TYR 0.006 0.001 TYR G 134 ARG 0.001 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.399 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.4765 time to fit residues: 50.7979 Evaluate side-chains 72 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8952 Z= 0.245 Angle : 0.477 4.085 12212 Z= 0.238 Chirality : 0.043 0.125 1360 Planarity : 0.003 0.048 1528 Dihedral : 10.846 69.115 1480 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.31 % Allowed : 20.85 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.24 (0.27), residues: 1112 helix: 0.12 (0.27), residues: 440 sheet: -1.86 (0.40), residues: 156 loop : -1.24 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 123 HIS 0.003 0.001 HIS G 196 PHE 0.010 0.001 PHE B 208 TYR 0.007 0.001 TYR B 149 ARG 0.001 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 1.412 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.5140 time to fit residues: 51.5111 Evaluate side-chains 74 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8952 Z= 0.132 Angle : 0.434 4.151 12212 Z= 0.214 Chirality : 0.041 0.127 1360 Planarity : 0.003 0.048 1528 Dihedral : 9.904 74.818 1480 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.76 % Allowed : 21.51 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.88 (0.27), residues: 1112 helix: 0.46 (0.27), residues: 440 sheet: -1.62 (0.43), residues: 148 loop : -1.12 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 64 HIS 0.002 0.000 HIS G 196 PHE 0.008 0.001 PHE G 208 TYR 0.008 0.001 TYR A 149 ARG 0.001 0.000 ARG F 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.5043 time to fit residues: 50.5722 Evaluate side-chains 69 residues out of total 916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.090033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.073623 restraints weight = 33387.323| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 1.88 r_work: 0.2538 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8952 Z= 0.166 Angle : 0.449 4.100 12212 Z= 0.222 Chirality : 0.042 0.128 1360 Planarity : 0.003 0.048 1528 Dihedral : 9.758 78.961 1480 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.76 % Allowed : 21.83 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.79 (0.27), residues: 1112 helix: 0.59 (0.27), residues: 440 sheet: -1.62 (0.43), residues: 148 loop : -1.10 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 64 HIS 0.003 0.001 HIS G 196 PHE 0.008 0.001 PHE B 208 TYR 0.007 0.001 TYR A 149 ARG 0.000 0.000 ARG G 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.11 seconds wall clock time: 67 minutes 46.87 seconds (4066.87 seconds total)