Starting phenix.real_space_refine on Tue Feb 3 18:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg8_61458/02_2026/9jg8_61458.cif" } resolution = 3.06 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 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= 0.159 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 3802 2.51 5 N 983 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6002 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1118 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain breaks: 2 Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1982 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain breaks: 6 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1863 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 219} Chain breaks: 3 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 352 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 343 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 343 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 487 SG CYS B 68 49.945 83.271 67.332 1.00109.60 S ATOM 697 SG CYS B 98 51.844 85.030 64.294 1.00 87.41 S ATOM 709 SG CYS B 100 53.717 85.616 66.855 1.00123.39 S Time building chain proxies: 1.04, per 1000 atoms: 0.17 Number of scatterers: 6002 At special positions: 0 Unit cell: (71.98, 99.12, 89.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 1169 8.00 N 983 7.00 C 3802 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 - 3.00 Amino acid : True - 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: 0.33 Conformation dependent library (CDL) restraints added in 294.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 98 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 68 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 100 " 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 14.1% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 375 through 379 removed outlier: 4.239A pdb=" N LEU C 379 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.832A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 142 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.442A pdb=" N ASP F 615 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N SER G 610 " --> pdb=" O ASP F 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 58 Processing sheet with id=AA4, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.056A pdb=" N ASP C 215 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR C 176 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.637A pdb=" N PHE C 150 " --> pdb=" O CYS C 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 256 through 263 removed outlier: 6.743A pdb=" N HIS C 291 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 260 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS C 289 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP C 262 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 287 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 279 through 280 removed outlier: 4.129A pdb=" N GLU C 357 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 318 removed outlier: 5.915A pdb=" N LEU C 315 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU C 357 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 50 through 56 removed outlier: 5.501A pdb=" N ARG A 51 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 32 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU A 53 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 30 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 50 through 56 removed outlier: 5.501A pdb=" N ARG A 51 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 32 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLU A 53 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE A 30 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.142A pdb=" N GLU A 91 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.640A pdb=" N ILE A 156 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 575 through 578 removed outlier: 6.509A pdb=" N LEU G 575 " --> pdb=" O MET F 584 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASP F 586 " --> pdb=" O LEU G 575 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL G 577 " --> pdb=" O ASP F 586 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR E 591 " --> pdb=" O TYR F 585 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA F 587 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR E 593 " --> pdb=" O ALA F 587 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS G 599 " --> pdb=" O LEU E 592 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA E 594 " --> pdb=" O LYS G 599 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU G 601 " --> pdb=" O ALA E 594 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET G 598 " --> pdb=" O GLY F 607 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LYS F 609 " --> pdb=" O MET G 598 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 600 " --> pdb=" O LYS F 609 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 607 through 610 removed outlier: 3.771A pdb=" N LEU F 601 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR G 591 " --> pdb=" O TYR E 585 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA E 587 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR G 593 " --> pdb=" O ALA E 587 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 558 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: 0.67 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1923 1.34 - 1.46: 1154 1.46 - 1.58: 2936 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 6089 Sorted by residual: bond pdb=" N ILE B 106 " pdb=" CA ILE B 106 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.24e+00 bond pdb=" N VAL A 233 " pdb=" CA VAL A 233 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.45e+00 bond pdb=" N ILE C 358 " pdb=" CA ILE C 358 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N VAL C 339 " pdb=" CA VAL C 339 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.48e+00 bond pdb=" N PHE A 220 " pdb=" CA PHE A 220 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.36e+00 ... (remaining 6084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 8032 2.18 - 4.36: 138 4.36 - 6.54: 11 6.54 - 8.71: 0 8.71 - 10.89: 1 Bond angle restraints: 8182 Sorted by residual: angle pdb=" O ASP C 389 " pdb=" C ASP C 389 " pdb=" N GLU C 390 " ideal model delta sigma weight residual 122.36 127.60 -5.24 1.42e+00 4.96e-01 1.36e+01 angle pdb=" CB MET B 12 " pdb=" CG MET B 12 " pdb=" SD MET B 12 " ideal model delta sigma weight residual 112.70 123.59 -10.89 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CA GLY C 386 " pdb=" C GLY C 386 " pdb=" O GLY C 386 " ideal model delta sigma weight residual 121.62 118.33 3.29 9.80e-01 1.04e+00 1.12e+01 angle pdb=" N CYS B 105 " pdb=" CA CYS B 105 " pdb=" C CYS B 105 " ideal model delta sigma weight residual 112.89 108.93 3.96 1.24e+00 6.50e-01 1.02e+01 angle pdb=" CA ALA C 388 " pdb=" C ALA C 388 " pdb=" O ALA C 388 " ideal model delta sigma weight residual 121.87 118.22 3.65 1.16e+00 7.43e-01 9.91e+00 ... (remaining 8177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3104 17.74 - 35.48: 411 35.48 - 53.22: 155 53.22 - 70.96: 21 70.96 - 88.70: 10 Dihedral angle restraints: 3701 sinusoidal: 1477 harmonic: 2224 Sorted by residual: dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA CYS A 160 " pdb=" C CYS A 160 " pdb=" N TYR A 161 " pdb=" CA TYR A 161 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU C 207 " pdb=" C LEU C 207 " pdb=" N GLN C 208 " pdb=" CA GLN C 208 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 626 0.037 - 0.073: 177 0.073 - 0.110: 83 0.110 - 0.147: 30 0.147 - 0.183: 6 Chirality restraints: 922 Sorted by residual: chirality pdb=" CA ILE C 242 " pdb=" N ILE C 242 " pdb=" C ILE C 242 " pdb=" CB ILE C 242 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA ILE B 106 " pdb=" N ILE B 106 " pdb=" C ILE B 106 " pdb=" CB ILE B 106 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 919 not shown) Planarity restraints: 1043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 183 " -0.013 2.00e-02 2.50e+03 1.03e-02 2.12e+00 pdb=" CG TYR C 183 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 183 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 183 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 183 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 183 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 183 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 183 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 139 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 69 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL B 69 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL B 69 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO B 70 " -0.008 2.00e-02 2.50e+03 ... (remaining 1040 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1831 2.83 - 3.34: 5125 3.34 - 3.86: 9839 3.86 - 4.38: 11632 4.38 - 4.90: 20461 Nonbonded interactions: 48888 Sorted by model distance: nonbonded pdb=" O PHE A 147 " pdb=" OH TYR A 152 " model vdw 2.308 3.040 nonbonded pdb=" OD1 ASP B 148 " pdb=" NZ LYS C 188 " model vdw 2.309 3.120 nonbonded pdb=" O ASP A 177 " pdb=" ND1 HIS A 190 " model vdw 2.326 3.120 nonbonded pdb=" O SER B 99 " pdb=" OG SER B 99 " model vdw 2.328 3.040 nonbonded pdb=" OD1 ASP B 138 " pdb=" OG SER C 187 " model vdw 2.331 3.040 ... (remaining 48883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 570 through 617) } 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: 8.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.004 0.037 6092 Z= 0.229 Angle : 0.620 10.892 8182 Z= 0.359 Chirality : 0.047 0.183 922 Planarity : 0.003 0.035 1043 Dihedral : 18.537 88.698 2269 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.30 % Allowed : 35.05 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.31), residues: 741 helix: 0.73 (0.59), residues: 89 sheet: -1.01 (0.38), residues: 180 loop : -1.75 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.025 0.001 TYR C 183 PHE 0.021 0.001 PHE C 356 TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6089) covalent geometry : angle 0.61986 ( 8182) hydrogen bonds : bond 0.14984 ( 189) hydrogen bonds : angle 7.22265 ( 558) metal coordination : bond 0.00624 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 395 LYS cc_start: 0.7235 (tttp) cc_final: 0.7005 (mtmt) outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.0621 time to fit residues: 9.3331 Evaluate side-chains 107 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0060 chunk 27 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN A 223 ASN F 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.176310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.160345 restraints weight = 7569.868| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.96 r_work: 0.3832 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6092 Z= 0.120 Angle : 0.518 6.395 8182 Z= 0.268 Chirality : 0.044 0.142 922 Planarity : 0.003 0.037 1043 Dihedral : 4.588 48.946 812 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.78 % Allowed : 31.42 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.31), residues: 741 helix: 1.27 (0.57), residues: 89 sheet: -0.72 (0.40), residues: 178 loop : -1.71 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.018 0.001 TYR C 183 PHE 0.015 0.001 PHE B 64 TRP 0.006 0.001 TRP C 262 HIS 0.001 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6089) covalent geometry : angle 0.51761 ( 8182) hydrogen bonds : bond 0.02970 ( 189) hydrogen bonds : angle 5.24039 ( 558) metal coordination : bond 0.00862 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 124 GLN cc_start: 0.7992 (mt0) cc_final: 0.7786 (mt0) REVERT: B 136 MET cc_start: 0.8052 (mmp) cc_final: 0.7620 (mmm) REVERT: A 52 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6880 (mt0) REVERT: A 215 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6841 (t) outliers start: 25 outliers final: 11 residues processed: 134 average time/residue: 0.0629 time to fit residues: 11.3550 Evaluate side-chains 121 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN F 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152360 restraints weight = 7541.836| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.09 r_work: 0.3739 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6092 Z= 0.221 Angle : 0.597 6.983 8182 Z= 0.310 Chirality : 0.046 0.159 922 Planarity : 0.004 0.039 1043 Dihedral : 5.024 46.515 812 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.04 % Allowed : 28.10 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.31), residues: 741 helix: 1.37 (0.57), residues: 89 sheet: -0.75 (0.40), residues: 177 loop : -1.73 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 277 TYR 0.020 0.002 TYR C 183 PHE 0.018 0.002 PHE C 150 TRP 0.006 0.002 TRP C 262 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 6089) covalent geometry : angle 0.59654 ( 8182) hydrogen bonds : bond 0.03396 ( 189) hydrogen bonds : angle 5.34687 ( 558) metal coordination : bond 0.00793 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7780 (tt0) cc_final: 0.7554 (tt0) REVERT: B 132 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: A 47 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: A 103 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 137 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7493 (mm-40) REVERT: G 590 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7199 (mtt) outliers start: 40 outliers final: 19 residues processed: 130 average time/residue: 0.0682 time to fit residues: 11.9299 Evaluate side-chains 125 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 590 MET Chi-restraints excluded: chain G residue 610 SER Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153657 restraints weight = 7588.632| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.08 r_work: 0.3756 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6092 Z= 0.160 Angle : 0.544 6.325 8182 Z= 0.281 Chirality : 0.045 0.140 922 Planarity : 0.004 0.038 1043 Dihedral : 4.865 45.815 812 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.53 % Allowed : 30.36 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.31), residues: 741 helix: 1.45 (0.58), residues: 89 sheet: -0.73 (0.40), residues: 177 loop : -1.71 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 153 TYR 0.016 0.002 TYR A 161 PHE 0.017 0.002 PHE B 64 TRP 0.006 0.002 TRP C 262 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6089) covalent geometry : angle 0.54352 ( 8182) hydrogen bonds : bond 0.02985 ( 189) hydrogen bonds : angle 5.11343 ( 558) metal coordination : bond 0.00939 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 132 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: B 144 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8465 (mtmt) REVERT: C 182 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: C 269 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7946 (ptmm) REVERT: A 103 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 137 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: A 142 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6918 (m-30) outliers start: 30 outliers final: 18 residues processed: 127 average time/residue: 0.0528 time to fit residues: 8.9631 Evaluate side-chains 126 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 610 SER Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147147 restraints weight = 7794.278| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.00 r_work: 0.3676 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 6092 Z= 0.363 Angle : 0.745 7.424 8182 Z= 0.389 Chirality : 0.052 0.207 922 Planarity : 0.005 0.041 1043 Dihedral : 5.767 47.992 812 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 6.95 % Allowed : 27.34 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.30), residues: 741 helix: 0.82 (0.57), residues: 89 sheet: -0.99 (0.40), residues: 176 loop : -2.00 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 153 TYR 0.027 0.003 TYR C 183 PHE 0.023 0.003 PHE C 150 TRP 0.008 0.003 TRP C 262 HIS 0.005 0.002 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00857 ( 6089) covalent geometry : angle 0.74462 ( 8182) hydrogen bonds : bond 0.04178 ( 189) hydrogen bonds : angle 5.80427 ( 558) metal coordination : bond 0.00990 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: B 132 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: C 182 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: C 209 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: A 44 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8255 (t80) REVERT: A 47 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 103 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 129 MET cc_start: 0.8722 (ttm) cc_final: 0.8327 (tpp) REVERT: A 137 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: A 142 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: E 582 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8092 (p0) outliers start: 46 outliers final: 29 residues processed: 136 average time/residue: 0.0469 time to fit residues: 8.6938 Evaluate side-chains 138 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 590 MET Chi-restraints excluded: chain G residue 610 SER Chi-restraints excluded: chain E residue 582 ASN Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151538 restraints weight = 7629.021| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.09 r_work: 0.3726 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6092 Z= 0.167 Angle : 0.570 6.372 8182 Z= 0.295 Chirality : 0.045 0.162 922 Planarity : 0.004 0.037 1043 Dihedral : 5.123 48.315 812 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.68 % Allowed : 29.46 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.30), residues: 741 helix: 1.11 (0.57), residues: 89 sheet: -0.87 (0.41), residues: 175 loop : -1.89 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.018 0.002 TYR C 183 PHE 0.019 0.001 PHE B 64 TRP 0.007 0.002 TRP C 262 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6089) covalent geometry : angle 0.56961 ( 8182) hydrogen bonds : bond 0.03030 ( 189) hydrogen bonds : angle 5.20627 ( 558) metal coordination : bond 0.01039 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: C 182 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 47 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 103 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 129 MET cc_start: 0.8852 (ttm) cc_final: 0.8436 (tpp) REVERT: A 137 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: A 142 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: A 157 ASP cc_start: 0.8479 (p0) cc_final: 0.8150 (p0) REVERT: E 582 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7961 (p0) outliers start: 31 outliers final: 19 residues processed: 128 average time/residue: 0.0685 time to fit residues: 11.7729 Evaluate side-chains 128 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain E residue 582 ASN Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN F 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154147 restraints weight = 7651.747| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.09 r_work: 0.3743 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6092 Z= 0.132 Angle : 0.534 6.451 8182 Z= 0.276 Chirality : 0.044 0.140 922 Planarity : 0.003 0.036 1043 Dihedral : 4.804 46.101 812 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.53 % Allowed : 29.15 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.31), residues: 741 helix: 1.24 (0.57), residues: 90 sheet: -0.85 (0.40), residues: 182 loop : -1.80 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.018 0.001 TYR A 76 PHE 0.020 0.001 PHE B 64 TRP 0.007 0.001 TRP C 262 HIS 0.001 0.000 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6089) covalent geometry : angle 0.53440 ( 8182) hydrogen bonds : bond 0.02725 ( 189) hydrogen bonds : angle 4.94213 ( 558) metal coordination : bond 0.00946 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7643 (tt0) cc_final: 0.7238 (tt0) REVERT: B 132 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: B 144 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (mtmt) REVERT: C 182 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 43 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.6109 (m-80) REVERT: A 47 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: A 103 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 129 MET cc_start: 0.8792 (ttm) cc_final: 0.8339 (tpp) REVERT: A 137 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: A 142 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: E 582 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7942 (p0) outliers start: 30 outliers final: 17 residues processed: 127 average time/residue: 0.0731 time to fit residues: 12.4139 Evaluate side-chains 130 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain E residue 582 ASN Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 610 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152025 restraints weight = 7604.992| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.06 r_work: 0.3719 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6092 Z= 0.179 Angle : 0.582 6.759 8182 Z= 0.301 Chirality : 0.046 0.163 922 Planarity : 0.004 0.036 1043 Dihedral : 4.975 43.790 812 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.68 % Allowed : 29.76 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.31), residues: 741 helix: 1.27 (0.57), residues: 89 sheet: -0.87 (0.40), residues: 182 loop : -1.80 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 153 TYR 0.017 0.002 TYR C 183 PHE 0.021 0.002 PHE B 64 TRP 0.007 0.002 TRP C 262 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6089) covalent geometry : angle 0.58228 ( 8182) hydrogen bonds : bond 0.03058 ( 189) hydrogen bonds : angle 5.05903 ( 558) metal coordination : bond 0.00988 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 132 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8076 (mm-30) REVERT: B 144 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8507 (mtmt) REVERT: C 182 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 43 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: A 47 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 103 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 129 MET cc_start: 0.8770 (ttm) cc_final: 0.8319 (tpp) REVERT: A 137 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: A 142 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: E 582 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7960 (p0) outliers start: 31 outliers final: 19 residues processed: 126 average time/residue: 0.0617 time to fit residues: 10.4762 Evaluate side-chains 130 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain E residue 582 ASN Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 610 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148251 restraints weight = 7722.130| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.09 r_work: 0.3687 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 6092 Z= 0.279 Angle : 0.682 8.336 8182 Z= 0.353 Chirality : 0.049 0.219 922 Planarity : 0.004 0.037 1043 Dihedral : 5.466 44.335 812 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.14 % Allowed : 29.31 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.30), residues: 741 helix: 0.95 (0.57), residues: 89 sheet: -0.81 (0.41), residues: 175 loop : -1.97 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 153 TYR 0.021 0.002 TYR C 183 PHE 0.021 0.002 PHE B 64 TRP 0.008 0.002 TRP A 102 HIS 0.004 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 6089) covalent geometry : angle 0.68163 ( 8182) hydrogen bonds : bond 0.03691 ( 189) hydrogen bonds : angle 5.45139 ( 558) metal coordination : bond 0.01138 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7843 (tt0) cc_final: 0.7543 (tt0) REVERT: B 132 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: B 144 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8566 (mtmt) REVERT: C 182 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 43 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: A 47 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: A 103 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7835 (mt-10) REVERT: A 129 MET cc_start: 0.8781 (ttm) cc_final: 0.8321 (tpp) REVERT: A 137 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 142 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: E 582 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8010 (p0) outliers start: 34 outliers final: 23 residues processed: 124 average time/residue: 0.0620 time to fit residues: 10.4644 Evaluate side-chains 132 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain E residue 582 ASN Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 588 GLN Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 610 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152725 restraints weight = 7611.152| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.09 r_work: 0.3736 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6092 Z= 0.150 Angle : 0.571 8.977 8182 Z= 0.294 Chirality : 0.045 0.161 922 Planarity : 0.004 0.036 1043 Dihedral : 4.977 44.021 812 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.93 % Allowed : 30.36 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.31), residues: 741 helix: 1.17 (0.57), residues: 89 sheet: -0.90 (0.39), residues: 182 loop : -1.84 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 166 TYR 0.017 0.002 TYR C 183 PHE 0.021 0.001 PHE B 64 TRP 0.007 0.001 TRP C 262 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6089) covalent geometry : angle 0.57120 ( 8182) hydrogen bonds : bond 0.02867 ( 189) hydrogen bonds : angle 5.05677 ( 558) metal coordination : bond 0.01019 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 5 GLU cc_start: 0.7710 (tt0) cc_final: 0.7440 (tt0) REVERT: B 132 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: B 144 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8518 (mtmt) REVERT: C 182 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 43 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: A 103 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 129 MET cc_start: 0.8796 (ttm) cc_final: 0.8339 (tpp) REVERT: A 137 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: A 142 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6949 (m-30) outliers start: 26 outliers final: 16 residues processed: 124 average time/residue: 0.0590 time to fit residues: 9.9596 Evaluate side-chains 127 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain F residue 571 ILE Chi-restraints excluded: chain F residue 584 MET Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 610 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 66 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN F 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154462 restraints weight = 7600.600| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.09 r_work: 0.3756 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6092 Z= 0.127 Angle : 0.550 8.860 8182 Z= 0.281 Chirality : 0.045 0.142 922 Planarity : 0.003 0.032 1043 Dihedral : 4.750 40.763 812 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.08 % Allowed : 30.06 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.31), residues: 741 helix: 1.28 (0.57), residues: 90 sheet: -0.77 (0.40), residues: 182 loop : -1.75 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.016 0.001 TYR C 183 PHE 0.022 0.001 PHE B 64 TRP 0.008 0.001 TRP C 262 HIS 0.002 0.000 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6089) covalent geometry : angle 0.54980 ( 8182) hydrogen bonds : bond 0.02685 ( 189) hydrogen bonds : angle 4.83678 ( 558) metal coordination : bond 0.00950 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.26 seconds wall clock time: 28 minutes 57.22 seconds (1737.22 seconds total)