Starting phenix.real_space_refine (version: dev) on Thu May 12 20:44:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz3_22529/05_2022/7jz3_22529_neut.pdb" } resolution = 2.56 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= 0.212 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8142 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Chain: "C" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2714 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 342} Time building chain proxies: 5.07, per 1000 atoms: 0.62 Number of scatterers: 8142 At special positions: 0 Unit cell: (93.96, 92.88, 71.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1662 8.00 N 1374 7.00 C 5097 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=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.2 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 6.4% alpha, 47.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.551A pdb=" N GLN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 4 through 5 current: chain 'B' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL B 75 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 59 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 73 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 61 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER B 71 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 91 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN B 93 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 126 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG B 217 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 244 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B 254 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 245 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP B 252 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 255 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 283 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 281 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 279 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY B 282 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 293 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 4 through 5 current: chain 'C' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL C 75 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C 59 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR C 73 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 61 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 71 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 91 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 93 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN C 126 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG C 217 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 244 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C 254 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 245 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP C 252 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 255 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 283 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 281 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 279 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 282 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP C 293 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 5 current: chain 'A' and resid 50 through 61 removed outlier: 3.584A pdb=" N VAL A 75 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 59 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 73 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 61 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 71 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 91 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 93 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 126 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N ARG A 217 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 244 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 254 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 245 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP A 252 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 255 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 283 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 281 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 279 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 265 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY A 282 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 293 " --> pdb=" O GLY A 282 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1089 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: 2.63 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2154 1.33 - 1.45: 1915 1.45 - 1.57: 4232 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8319 Sorted by residual: bond pdb=" CA ASN C 133 " pdb=" CB ASN C 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.37e+00 bond pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.55e-02 4.16e+03 6.26e+00 bond pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta sigma weight residual 1.530 1.492 0.039 1.55e-02 4.16e+03 6.21e+00 bond pdb=" N ASN C 133 " pdb=" CA ASN C 133 " ideal model delta sigma weight residual 1.455 1.427 0.028 1.22e-02 6.72e+03 5.39e+00 bond pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta sigma weight residual 1.455 1.428 0.028 1.22e-02 6.72e+03 5.11e+00 ... (remaining 8314 not shown) Histogram of bond angle deviations from ideal: 101.02 - 107.62: 151 107.62 - 114.22: 4230 114.22 - 120.82: 3613 120.82 - 127.42: 3238 127.42 - 134.02: 33 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N VAL B 29 " pdb=" CA VAL B 29 " pdb=" C VAL B 29 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N VAL C 29 " pdb=" CA VAL C 29 " pdb=" C VAL C 29 " ideal model delta sigma weight residual 113.53 109.83 3.70 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 113.53 109.85 3.68 9.80e-01 1.04e+00 1.41e+01 angle pdb=" N GLY C 138 " pdb=" CA GLY C 138 " pdb=" C GLY C 138 " ideal model delta sigma weight residual 115.32 119.34 -4.02 1.38e+00 5.25e-01 8.49e+00 angle pdb=" N GLY B 138 " pdb=" CA GLY B 138 " pdb=" C GLY B 138 " ideal model delta sigma weight residual 115.32 119.33 -4.01 1.38e+00 5.25e-01 8.43e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4233 16.34 - 32.69: 365 32.69 - 49.03: 88 49.03 - 65.37: 15 65.37 - 81.71: 6 Dihedral angle restraints: 4707 sinusoidal: 1791 harmonic: 2916 Sorted by residual: dihedral pdb=" CA GLN A 237 " pdb=" CB GLN A 237 " pdb=" CG GLN A 237 " pdb=" CD GLN A 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.89 50.89 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " pdb=" CD GLN B 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.88 50.88 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA GLN C 237 " pdb=" CB GLN C 237 " pdb=" CG GLN C 237 " pdb=" CD GLN C 237 " ideal model delta sinusoidal sigma weight residual -60.00 -110.86 50.86 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 4704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 722 0.037 - 0.073: 279 0.073 - 0.110: 91 0.110 - 0.147: 30 0.147 - 0.183: 6 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PHE C 136 " pdb=" N PHE C 136 " pdb=" C PHE C 136 " pdb=" CB PHE C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE B 136 " pdb=" N PHE B 136 " pdb=" C PHE B 136 " pdb=" CB PHE B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" CA PHE A 136 " pdb=" N PHE A 136 " pdb=" C PHE A 136 " pdb=" CB PHE A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1125 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 84 " -0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" CG ASP A 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 84 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" CG ASP C 84 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP C 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 84 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 84 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" CG ASP B 84 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP B 84 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 838 2.75 - 3.29: 7936 3.29 - 3.82: 13672 3.82 - 4.36: 17117 4.36 - 4.90: 30181 Nonbonded interactions: 69744 Sorted by model distance: nonbonded pdb=" NE2 GLN B 237 " pdb=" OG1 THR B 239 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN C 237 " pdb=" OG1 THR C 239 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN A 237 " pdb=" OG1 THR A 239 " model vdw 2.211 2.520 nonbonded pdb=" OD2 ASP A 89 " pdb=" ND2 ASN A 93 " model vdw 2.288 2.520 nonbonded pdb=" OD2 ASP B 89 " pdb=" ND2 ASN B 93 " model vdw 2.289 2.520 ... (remaining 69739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 5097 2.51 5 N 1374 2.21 5 O 1662 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: 0.070 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: 0.000 Extract box with map and model: 1.220 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 24.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 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 : 0.003 0.039 8319 Z= 0.213 Angle : 0.623 6.968 11265 Z= 0.384 Chirality : 0.046 0.183 1128 Planarity : 0.003 0.038 1530 Dihedral : 13.643 81.714 2913 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.54 (0.23), residues: 1032 helix: -2.59 (0.66), residues: 42 sheet: -0.80 (0.20), residues: 561 loop : -2.78 (0.24), residues: 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 0.847 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 203 average time/residue: 0.7975 time to fit residues: 175.9061 Evaluate side-chains 153 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 21 HIS B 45 GLN B 61 GLN B 83 GLN B 144 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 9 ASN C 21 HIS C 45 GLN C 61 GLN C 69 ASN C 144 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 ASN A 21 HIS A 45 GLN A 61 GLN A 69 ASN A 144 ASN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 319 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 8319 Z= 0.460 Angle : 0.877 12.473 11265 Z= 0.470 Chirality : 0.053 0.162 1128 Planarity : 0.005 0.050 1530 Dihedral : 5.694 19.414 1164 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.23), residues: 1032 helix: -3.10 (0.40), residues: 60 sheet: -0.61 (0.21), residues: 543 loop : -3.10 (0.24), residues: 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 0.898 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 27 residues processed: 203 average time/residue: 0.7635 time to fit residues: 168.9077 Evaluate side-chains 188 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 14 residues processed: 13 average time/residue: 0.4467 time to fit residues: 7.8303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8319 Z= 0.245 Angle : 0.690 9.566 11265 Z= 0.370 Chirality : 0.047 0.175 1128 Planarity : 0.004 0.053 1530 Dihedral : 5.116 17.734 1164 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 6.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.25 (0.24), residues: 1032 helix: -2.06 (0.63), residues: 60 sheet: -0.47 (0.21), residues: 552 loop : -2.81 (0.25), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 0.891 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 204 average time/residue: 0.7450 time to fit residues: 166.2097 Evaluate side-chains 190 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 24 residues processed: 12 average time/residue: 0.1714 time to fit residues: 3.9176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 62 optimal weight: 0.0670 chunk 93 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8319 Z= 0.214 Angle : 0.663 9.035 11265 Z= 0.352 Chirality : 0.046 0.160 1128 Planarity : 0.004 0.057 1530 Dihedral : 4.892 17.204 1164 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 7.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.05 (0.24), residues: 1032 helix: -1.92 (0.67), residues: 60 sheet: -0.35 (0.21), residues: 552 loop : -2.67 (0.26), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 170 time to evaluate : 1.000 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 40 residues processed: 209 average time/residue: 0.7699 time to fit residues: 175.4611 Evaluate side-chains 199 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 14 average time/residue: 0.3651 time to fit residues: 7.2295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8319 Z= 0.202 Angle : 0.650 8.867 11265 Z= 0.345 Chirality : 0.045 0.134 1128 Planarity : 0.004 0.054 1530 Dihedral : 4.777 17.035 1164 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.77 (0.25), residues: 1032 helix: -1.52 (0.79), residues: 42 sheet: -0.25 (0.21), residues: 552 loop : -2.37 (0.26), residues: 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 38 residues processed: 201 average time/residue: 0.7279 time to fit residues: 161.2571 Evaluate side-chains 198 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 11 average time/residue: 0.1981 time to fit residues: 4.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 8319 Z= 0.331 Angle : 0.762 8.995 11265 Z= 0.408 Chirality : 0.048 0.190 1128 Planarity : 0.005 0.056 1530 Dihedral : 5.290 19.273 1164 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 7.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.25), residues: 1032 helix: -1.67 (0.75), residues: 42 sheet: -0.28 (0.22), residues: 549 loop : -2.54 (0.26), residues: 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 202 average time/residue: 0.7565 time to fit residues: 167.2040 Evaluate side-chains 202 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 28 residues processed: 14 average time/residue: 0.2735 time to fit residues: 5.8900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 144 ASN A 148 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 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 : 0.005 0.045 8319 Z= 0.319 Angle : 0.767 8.875 11265 Z= 0.408 Chirality : 0.048 0.189 1128 Planarity : 0.005 0.054 1530 Dihedral : 5.303 19.248 1164 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 6.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.25), residues: 1032 helix: -1.59 (0.74), residues: 42 sheet: -0.23 (0.22), residues: 543 loop : -2.58 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 0.869 Fit side-chains outliers start: 57 outliers final: 43 residues processed: 195 average time/residue: 0.6964 time to fit residues: 149.4826 Evaluate side-chains 199 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 31 residues processed: 13 average time/residue: 0.1658 time to fit residues: 4.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN C 83 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 8319 Z= 0.332 Angle : 0.782 8.796 11265 Z= 0.417 Chirality : 0.048 0.179 1128 Planarity : 0.005 0.052 1530 Dihedral : 5.381 19.601 1164 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 7.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.25), residues: 1032 helix: -1.70 (0.72), residues: 42 sheet: -0.28 (0.22), residues: 543 loop : -2.62 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 159 time to evaluate : 0.815 Fit side-chains outliers start: 61 outliers final: 48 residues processed: 198 average time/residue: 0.7257 time to fit residues: 157.4977 Evaluate side-chains 201 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 33 residues processed: 16 average time/residue: 0.2197 time to fit residues: 5.6779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8319 Z= 0.269 Angle : 0.739 8.613 11265 Z= 0.394 Chirality : 0.047 0.152 1128 Planarity : 0.004 0.053 1530 Dihedral : 5.174 20.503 1164 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.25), residues: 1032 helix: -1.37 (0.79), residues: 42 sheet: -0.32 (0.22), residues: 543 loop : -2.44 (0.27), residues: 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 0.798 Fit side-chains outliers start: 51 outliers final: 42 residues processed: 195 average time/residue: 0.6698 time to fit residues: 143.8961 Evaluate side-chains 193 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 34 residues processed: 9 average time/residue: 0.3192 time to fit residues: 4.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 8319 Z= 0.393 Angle : 0.837 8.757 11265 Z= 0.448 Chirality : 0.050 0.200 1128 Planarity : 0.005 0.052 1530 Dihedral : 5.589 22.234 1164 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 6.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.25), residues: 1032 helix: -1.92 (0.69), residues: 42 sheet: -0.40 (0.22), residues: 549 loop : -2.59 (0.26), residues: 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 0.847 Fit side-chains outliers start: 52 outliers final: 40 residues processed: 192 average time/residue: 0.7281 time to fit residues: 155.3338 Evaluate side-chains 187 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 9 average time/residue: 0.3259 time to fit residues: 4.8604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN B 148 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.247563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.236207 restraints weight = 9663.666| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 1.78 r_work: 0.4705 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4697 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.4688 rms_B_bonded: 1.71 restraints_weight: 0.1250 r_work: 0.4679 rms_B_bonded: 1.85 restraints_weight: 0.0625 r_work: 0.4669 rms_B_bonded: 2.04 restraints_weight: 0.0312 r_work: 0.4657 rms_B_bonded: 2.28 restraints_weight: 0.0156 r_work: 0.4645 rms_B_bonded: 2.56 restraints_weight: 0.0078 r_work: 0.4631 rms_B_bonded: 2.89 restraints_weight: 0.0039 r_work: 0.4617 rms_B_bonded: 3.28 restraints_weight: 0.0020 r_work: 0.4600 rms_B_bonded: 3.74 restraints_weight: 0.0010 r_work: 0.4581 rms_B_bonded: 4.26 restraints_weight: 0.0005 r_work: 0.4561 rms_B_bonded: 4.86 restraints_weight: 0.0002 r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.069 8319 Z= 0.499 Angle : 0.936 9.587 11265 Z= 0.504 Chirality : 0.053 0.278 1128 Planarity : 0.006 0.061 1530 Dihedral : 6.013 23.076 1164 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 6.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.25), residues: 1032 helix: -2.47 (0.64), residues: 42 sheet: -0.47 (0.22), residues: 543 loop : -2.88 (0.25), residues: 447 =============================================================================== Job complete usr+sys time: 2854.64 seconds wall clock time: 51 minutes 26.27 seconds (3086.27 seconds total)