Starting phenix.real_space_refine on Fri Jul 19 03:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyh_42806/07_2024/8uyh_42806_neut.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 40 5.16 5 C 3840 2.51 5 N 1013 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3003 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 6 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2968 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 352} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.97, per 1000 atoms: 0.66 Number of scatterers: 6036 At special positions: 0 Unit cell: (116.352, 81.608, 72.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 8 15.00 Mg 3 11.99 O 1132 8.00 N 1013 7.00 C 3840 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: 2.26 Conformation dependent library (CDL) restraints added in 979.7 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 46.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.577A pdb=" N GLU A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.559A pdb=" N THR A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.659A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.681A pdb=" N CYS A 360 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.590A pdb=" N GLY A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.580A pdb=" N LEU A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.609A pdb=" N THR B 215 " --> pdb=" O MET B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.710A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.562A pdb=" N CYS B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.519A pdb=" N GLY B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 414 " --> pdb=" O TRP B 410 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.703A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.587A pdb=" N VAL A 173 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS A 167 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.454A pdb=" N GLY B 162 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LYS B 177 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER B 175 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER B 285 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR B 250 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 254 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.708A pdb=" N CYS B 295 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372 276 hydrogen bonds defined for protein. 789 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: 1.59 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1920 1.34 - 1.46: 1237 1.46 - 1.58: 2917 1.58 - 1.69: 16 1.69 - 1.81: 62 Bond restraints: 6152 Sorted by residual: bond pdb=" O3A ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 6147 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 213 107.18 - 113.90: 3520 113.90 - 120.61: 2276 120.61 - 127.32: 2263 127.32 - 134.04: 70 Bond angle restraints: 8342 Sorted by residual: angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 109.08 17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" PB ANP A 601 " pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 126.95 109.87 17.08 3.00e+00 1.11e-01 3.24e+01 angle pdb=" CB TPO A 305 " pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 119.31 107.60 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB TPO B 305 " pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 119.31 107.87 11.44 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O1B ANP A 601 " pdb=" PB ANP A 601 " pdb=" O2B ANP A 601 " ideal model delta sigma weight residual 120.08 109.30 10.78 3.00e+00 1.11e-01 1.29e+01 ... (remaining 8337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 3605 21.93 - 43.87: 118 43.87 - 65.80: 30 65.80 - 87.73: 23 87.73 - 109.66: 1 Dihedral angle restraints: 3777 sinusoidal: 1570 harmonic: 2207 Sorted by residual: dihedral pdb=" O1B ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PB ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sinusoidal sigma weight residual 35.15 -74.51 109.66 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA LEU A 483 " pdb=" C LEU A 483 " pdb=" N TRP A 484 " pdb=" CA TRP A 484 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.89e+00 dihedral pdb=" N GLU B 376 " pdb=" CA GLU B 376 " pdb=" CB GLU B 376 " pdb=" CG GLU B 376 " ideal model delta sinusoidal sigma weight residual -180.00 -120.43 -59.57 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 801 0.055 - 0.111: 123 0.111 - 0.166: 17 0.166 - 0.221: 0 0.221 - 0.277: 2 Chirality restraints: 943 Sorted by residual: chirality pdb=" C3' ANP B 601 " pdb=" C2' ANP B 601 " pdb=" C4' ANP B 601 " pdb=" O3' ANP B 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 940 not shown) Planarity restraints: 1038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO B 451 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 450 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 451 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 243 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO B 244 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.025 5.00e-02 4.00e+02 ... (remaining 1035 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 68 2.64 - 3.20: 4957 3.20 - 3.77: 9004 3.77 - 4.33: 13307 4.33 - 4.90: 21614 Nonbonded interactions: 48950 Sorted by model distance: nonbonded pdb=" O2B ANP B 601 " pdb="MG MG B 602 " model vdw 2.074 2.170 nonbonded pdb=" OD2 ASP B 357 " pdb="MG MG B 603 " model vdw 2.131 2.170 nonbonded pdb=" N3B ANP A 601 " pdb="MG MG A 602 " model vdw 2.238 2.250 nonbonded pdb=" O THR A 215 " pdb=" OH TYR A 221 " model vdw 2.280 2.440 nonbonded pdb=" O2B ANP A 601 " pdb="MG MG A 602 " model vdw 2.321 2.170 ... (remaining 48945 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' and (resid 121 through 223 or resid 238 through 515 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574 o \ r resid 601 through 602)) selection = (chain 'B' and (resid 121 through 136 or resid 148 through 427 or (resid 432 and \ (name N or name CA or name C or name O or name CB )) or resid 433 through 540 o \ r resid 542 through 574 or resid 601 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 : 0.006 0.142 6152 Z= 0.305 Angle : 0.763 17.873 8342 Z= 0.361 Chirality : 0.042 0.277 943 Planarity : 0.005 0.050 1038 Dihedral : 13.962 109.665 2333 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % 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: -1.53 (0.27), residues: 711 helix: -1.14 (0.21), residues: 307 sheet: -1.13 (0.49), residues: 103 loop : -0.58 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 484 HIS 0.003 0.001 HIS A 328 PHE 0.010 0.001 PHE B 253 TYR 0.011 0.001 TYR A 494 ARG 0.002 0.000 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 0.611 Fit side-chains REVERT: A 167 LYS cc_start: 0.7289 (mttt) cc_final: 0.6642 (mttp) REVERT: A 177 LYS cc_start: 0.6773 (tttt) cc_final: 0.6474 (ttpp) REVERT: A 189 GLN cc_start: 0.7291 (mt0) cc_final: 0.7081 (mm110) REVERT: A 211 MET cc_start: 0.8201 (mtt) cc_final: 0.7979 (mtt) REVERT: A 248 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7211 (ttm170) REVERT: A 300 TYR cc_start: 0.7999 (t80) cc_final: 0.7729 (t80) REVERT: A 343 ASP cc_start: 0.7352 (t0) cc_final: 0.7140 (t0) REVERT: A 346 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6164 (mp0) REVERT: A 350 TYR cc_start: 0.7705 (m-80) cc_final: 0.7345 (m-80) REVERT: A 545 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6534 (mt-10) REVERT: A 554 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7658 (mtt-85) REVERT: B 133 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7430 (mm-30) REVERT: B 167 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7524 (mppt) REVERT: B 177 LYS cc_start: 0.7401 (pttt) cc_final: 0.7129 (mtmm) REVERT: B 189 GLN cc_start: 0.7820 (mt0) cc_final: 0.7124 (mm110) REVERT: B 201 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6981 (mp0) REVERT: B 212 TYR cc_start: 0.7892 (t80) cc_final: 0.6540 (m-10) REVERT: B 290 MET cc_start: 0.8586 (mtm) cc_final: 0.8360 (mtp) REVERT: B 510 SER cc_start: 0.8833 (p) cc_final: 0.8418 (m) outliers start: 10 outliers final: 1 residues processed: 182 average time/residue: 1.1005 time to fit residues: 209.6707 Evaluate side-chains 139 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN A 569 GLN B 197 ASN B 572 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6152 Z= 0.239 Angle : 0.541 6.126 8342 Z= 0.275 Chirality : 0.042 0.154 943 Planarity : 0.005 0.047 1038 Dihedral : 10.733 91.901 867 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.30 % Allowed : 11.36 % Favored : 83.33 % 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: 0.23 (0.30), residues: 711 helix: 1.18 (0.27), residues: 308 sheet: -0.82 (0.49), residues: 96 loop : -0.49 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 129 HIS 0.004 0.001 HIS B 324 PHE 0.014 0.002 PHE A 196 TYR 0.015 0.001 TYR B 221 ARG 0.007 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 0.688 Fit side-chains REVERT: A 167 LYS cc_start: 0.7310 (mttt) cc_final: 0.6637 (mttp) REVERT: A 177 LYS cc_start: 0.6972 (tttt) cc_final: 0.6580 (ttpp) REVERT: A 214 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8282 (mm-30) REVERT: A 248 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7032 (tpp-160) REVERT: A 300 TYR cc_start: 0.7891 (t80) cc_final: 0.7533 (t80) REVERT: A 376 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: A 379 ASP cc_start: 0.7724 (p0) cc_final: 0.7398 (p0) REVERT: A 554 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7123 (mtp-110) REVERT: A 566 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7289 (mtpt) REVERT: B 167 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7493 (mppt) REVERT: B 177 LYS cc_start: 0.7451 (pttt) cc_final: 0.7251 (mtmm) REVERT: B 189 GLN cc_start: 0.7846 (mt0) cc_final: 0.7038 (mm110) REVERT: B 201 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7192 (mp0) REVERT: B 212 TYR cc_start: 0.7899 (t80) cc_final: 0.6419 (m-10) REVERT: B 239 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6993 (mtp85) REVERT: B 423 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7569 (t70) REVERT: B 436 LYS cc_start: 0.7419 (tttt) cc_final: 0.7057 (tttp) REVERT: B 439 LYS cc_start: 0.7827 (mttt) cc_final: 0.7560 (mtpp) REVERT: B 498 ASN cc_start: 0.6705 (p0) cc_final: 0.5946 (p0) REVERT: B 501 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 510 SER cc_start: 0.8853 (p) cc_final: 0.8470 (m) REVERT: B 541 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6551 (mpt-90) outliers start: 35 outliers final: 8 residues processed: 154 average time/residue: 1.1385 time to fit residues: 183.8249 Evaluate side-chains 143 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6152 Z= 0.141 Angle : 0.445 4.904 8342 Z= 0.227 Chirality : 0.039 0.145 943 Planarity : 0.004 0.045 1038 Dihedral : 8.739 88.209 865 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.00 % Allowed : 13.03 % Favored : 81.97 % 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: 0.93 (0.31), residues: 711 helix: 2.05 (0.28), residues: 310 sheet: -0.58 (0.49), residues: 96 loop : -0.45 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.003 0.001 HIS A 328 PHE 0.011 0.001 PHE A 253 TYR 0.011 0.001 TYR B 174 ARG 0.006 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 167 LYS cc_start: 0.7417 (mttt) cc_final: 0.6717 (mttp) REVERT: A 177 LYS cc_start: 0.7013 (tttt) cc_final: 0.6531 (ttpp) REVERT: A 248 ARG cc_start: 0.7479 (ttt90) cc_final: 0.7096 (tpp-160) REVERT: A 300 TYR cc_start: 0.7801 (t80) cc_final: 0.7512 (t80) REVERT: A 376 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: A 379 ASP cc_start: 0.7722 (p0) cc_final: 0.7444 (p0) REVERT: A 554 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7092 (mtp-110) REVERT: A 566 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.6965 (mtpt) REVERT: B 167 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7474 (mppt) REVERT: B 177 LYS cc_start: 0.7532 (pttt) cc_final: 0.7300 (mtmm) REVERT: B 189 GLN cc_start: 0.7890 (mt0) cc_final: 0.7052 (mm-40) REVERT: B 196 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6574 (p90) REVERT: B 201 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 212 TYR cc_start: 0.7904 (t80) cc_final: 0.6354 (m-10) REVERT: B 239 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7080 (mtp85) REVERT: B 423 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7554 (t70) REVERT: B 436 LYS cc_start: 0.7356 (tttt) cc_final: 0.6913 (tttp) REVERT: B 472 CYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7195 (p) REVERT: B 510 SER cc_start: 0.8846 (p) cc_final: 0.8520 (m) REVERT: B 541 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6597 (mpt-90) outliers start: 33 outliers final: 9 residues processed: 151 average time/residue: 1.0962 time to fit residues: 173.6807 Evaluate side-chains 144 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6152 Z= 0.184 Angle : 0.459 5.057 8342 Z= 0.235 Chirality : 0.040 0.141 943 Planarity : 0.004 0.045 1038 Dihedral : 8.449 90.511 865 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.15 % Allowed : 14.24 % Favored : 80.61 % 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: 1.15 (0.32), residues: 711 helix: 2.28 (0.29), residues: 310 sheet: -0.44 (0.49), residues: 96 loop : -0.40 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 129 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE B 452 TYR 0.010 0.001 TYR A 482 ARG 0.005 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 0.675 Fit side-chains REVERT: A 124 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7101 (mt) REVERT: A 167 LYS cc_start: 0.7455 (mttt) cc_final: 0.6753 (mttp) REVERT: A 177 LYS cc_start: 0.7115 (tttt) cc_final: 0.6628 (ttpp) REVERT: A 248 ARG cc_start: 0.7466 (ttt90) cc_final: 0.7104 (tpp-160) REVERT: A 302 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6526 (ttp-110) REVERT: A 376 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 379 ASP cc_start: 0.7713 (p0) cc_final: 0.7455 (p0) REVERT: A 554 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7538 (mtt180) REVERT: A 566 LYS cc_start: 0.7809 (mtpt) cc_final: 0.6975 (mtpt) REVERT: B 177 LYS cc_start: 0.7588 (pttt) cc_final: 0.7347 (mtmm) REVERT: B 189 GLN cc_start: 0.7872 (mt0) cc_final: 0.7023 (mm-40) REVERT: B 196 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.6593 (p90) REVERT: B 201 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 212 TYR cc_start: 0.7938 (t80) cc_final: 0.6333 (m-10) REVERT: B 239 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7058 (mtp85) REVERT: B 423 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7553 (t70) REVERT: B 436 LYS cc_start: 0.7391 (tttt) cc_final: 0.6949 (tttp) REVERT: B 439 LYS cc_start: 0.7821 (mttt) cc_final: 0.7542 (mtpp) REVERT: B 473 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6175 (t0) REVERT: B 504 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: B 510 SER cc_start: 0.8842 (p) cc_final: 0.8494 (m) REVERT: B 541 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6650 (mpt-90) REVERT: B 570 GLU cc_start: 0.7129 (pp20) cc_final: 0.6748 (tm-30) outliers start: 34 outliers final: 12 residues processed: 149 average time/residue: 1.0868 time to fit residues: 169.9871 Evaluate side-chains 152 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6152 Z= 0.225 Angle : 0.481 5.262 8342 Z= 0.247 Chirality : 0.040 0.141 943 Planarity : 0.004 0.046 1038 Dihedral : 8.505 91.554 865 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.15 % Allowed : 15.15 % Favored : 79.70 % 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: 1.21 (0.32), residues: 711 helix: 2.40 (0.29), residues: 308 sheet: -0.45 (0.49), residues: 96 loop : -0.42 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 129 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.002 PHE A 253 TYR 0.010 0.001 TYR A 482 ARG 0.003 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7103 (mt) REVERT: A 167 LYS cc_start: 0.7443 (mttt) cc_final: 0.6716 (mttp) REVERT: A 177 LYS cc_start: 0.7111 (tttt) cc_final: 0.6676 (ttpp) REVERT: A 248 ARG cc_start: 0.7461 (ttt90) cc_final: 0.7076 (tpp-160) REVERT: A 302 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6530 (ttp-110) REVERT: A 308 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6610 (tpp) REVERT: A 376 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: A 379 ASP cc_start: 0.7725 (p0) cc_final: 0.7484 (p0) REVERT: A 418 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: A 554 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7549 (mtt180) REVERT: A 566 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6990 (mtpt) REVERT: B 177 LYS cc_start: 0.7587 (pttt) cc_final: 0.7344 (mtmm) REVERT: B 189 GLN cc_start: 0.7803 (mt0) cc_final: 0.6948 (mm-40) REVERT: B 196 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6522 (p90) REVERT: B 201 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 212 TYR cc_start: 0.7856 (t80) cc_final: 0.6257 (m-10) REVERT: B 239 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7068 (mtp85) REVERT: B 423 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7586 (t70) REVERT: B 436 LYS cc_start: 0.7407 (tttt) cc_final: 0.6909 (tttp) REVERT: B 439 LYS cc_start: 0.7842 (mttt) cc_final: 0.7557 (mtpp) REVERT: B 473 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6218 (t0) REVERT: B 510 SER cc_start: 0.8825 (p) cc_final: 0.8455 (m) REVERT: B 541 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6683 (mpt-90) REVERT: B 570 GLU cc_start: 0.7118 (pp20) cc_final: 0.6730 (tm-30) outliers start: 34 outliers final: 15 residues processed: 150 average time/residue: 1.1267 time to fit residues: 177.1496 Evaluate side-chains 152 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6152 Z= 0.240 Angle : 0.486 5.012 8342 Z= 0.249 Chirality : 0.041 0.138 943 Planarity : 0.004 0.047 1038 Dihedral : 8.608 92.999 865 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.45 % Allowed : 15.76 % Favored : 78.79 % 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: 1.21 (0.32), residues: 711 helix: 2.44 (0.29), residues: 308 sheet: -0.50 (0.49), residues: 96 loop : -0.43 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 129 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.002 PHE A 253 TYR 0.010 0.001 TYR A 482 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 0.713 Fit side-chains REVERT: A 124 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7114 (mt) REVERT: A 167 LYS cc_start: 0.7443 (mttt) cc_final: 0.6685 (mttp) REVERT: A 177 LYS cc_start: 0.7178 (tttt) cc_final: 0.6732 (ttpp) REVERT: A 214 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: A 248 ARG cc_start: 0.7444 (ttt90) cc_final: 0.7033 (tpp-160) REVERT: A 302 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6616 (ttp-110) REVERT: A 376 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: A 379 ASP cc_start: 0.7709 (p0) cc_final: 0.7459 (p0) REVERT: A 418 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: A 554 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7566 (mtt180) REVERT: A 566 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6999 (mtpt) REVERT: B 177 LYS cc_start: 0.7615 (pttt) cc_final: 0.7371 (mtmm) REVERT: B 189 GLN cc_start: 0.7835 (mt0) cc_final: 0.6962 (mm-40) REVERT: B 196 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.6559 (p90) REVERT: B 201 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 212 TYR cc_start: 0.7893 (t80) cc_final: 0.6243 (m-10) REVERT: B 239 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7083 (mtp85) REVERT: B 423 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7606 (t70) REVERT: B 436 LYS cc_start: 0.7397 (tttt) cc_final: 0.6906 (tttp) REVERT: B 439 LYS cc_start: 0.7861 (mttt) cc_final: 0.7567 (mtpp) REVERT: B 473 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6166 (t0) REVERT: B 510 SER cc_start: 0.8862 (p) cc_final: 0.8482 (m) REVERT: B 541 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6714 (mpt-90) REVERT: B 570 GLU cc_start: 0.7232 (pp20) cc_final: 0.6696 (tm-30) outliers start: 36 outliers final: 13 residues processed: 148 average time/residue: 1.0995 time to fit residues: 171.0732 Evaluate side-chains 153 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 155 ASN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6152 Z= 0.151 Angle : 0.444 5.259 8342 Z= 0.226 Chirality : 0.039 0.143 943 Planarity : 0.004 0.047 1038 Dihedral : 8.390 95.264 865 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.55 % Allowed : 17.12 % Favored : 78.33 % 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: 1.38 (0.32), residues: 711 helix: 2.56 (0.29), residues: 309 sheet: -0.52 (0.49), residues: 98 loop : -0.30 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 129 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.001 PHE A 253 TYR 0.008 0.001 TYR A 482 ARG 0.003 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.654 Fit side-chains REVERT: A 124 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7100 (mt) REVERT: A 167 LYS cc_start: 0.7456 (mttt) cc_final: 0.6680 (mttp) REVERT: A 177 LYS cc_start: 0.7231 (tttt) cc_final: 0.6802 (ttpp) REVERT: A 214 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8248 (mm-30) REVERT: A 248 ARG cc_start: 0.7406 (ttt90) cc_final: 0.7005 (tpp-160) REVERT: A 300 TYR cc_start: 0.7803 (t80) cc_final: 0.7588 (t80) REVERT: A 302 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6621 (ttp-110) REVERT: A 308 MET cc_start: 0.6923 (tpt) cc_final: 0.6643 (tpp) REVERT: A 376 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: A 379 ASP cc_start: 0.7694 (p0) cc_final: 0.7466 (p0) REVERT: A 554 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7556 (mtt180) REVERT: A 566 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6961 (mtpt) REVERT: B 177 LYS cc_start: 0.7566 (pttt) cc_final: 0.7327 (mtmm) REVERT: B 189 GLN cc_start: 0.7832 (mt0) cc_final: 0.6958 (mm-40) REVERT: B 196 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6552 (p90) REVERT: B 201 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 212 TYR cc_start: 0.7885 (t80) cc_final: 0.6231 (m-10) REVERT: B 239 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: B 423 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7595 (t70) REVERT: B 436 LYS cc_start: 0.7358 (tttt) cc_final: 0.6867 (tttp) REVERT: B 439 LYS cc_start: 0.7836 (mttt) cc_final: 0.7578 (mtpp) REVERT: B 504 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7525 (mp10) REVERT: B 510 SER cc_start: 0.8827 (p) cc_final: 0.8458 (m) REVERT: B 541 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6737 (mpt-90) REVERT: B 570 GLU cc_start: 0.7211 (pp20) cc_final: 0.6769 (tm-30) outliers start: 30 outliers final: 14 residues processed: 149 average time/residue: 1.0972 time to fit residues: 171.7823 Evaluate side-chains 151 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 155 ASN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6152 Z= 0.257 Angle : 0.501 5.437 8342 Z= 0.255 Chirality : 0.041 0.145 943 Planarity : 0.004 0.048 1038 Dihedral : 8.492 94.690 865 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.30 % Allowed : 17.12 % Favored : 77.58 % 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: 1.29 (0.32), residues: 711 helix: 2.46 (0.29), residues: 309 sheet: -0.53 (0.49), residues: 98 loop : -0.32 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 129 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.002 PHE A 253 TYR 0.010 0.001 TYR A 482 ARG 0.003 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 0.692 Fit side-chains REVERT: A 124 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7094 (mt) REVERT: A 167 LYS cc_start: 0.7512 (mttt) cc_final: 0.6732 (mttp) REVERT: A 177 LYS cc_start: 0.7276 (tttt) cc_final: 0.6878 (ttpp) REVERT: A 248 ARG cc_start: 0.7411 (ttt90) cc_final: 0.6985 (tpp-160) REVERT: A 302 ARG cc_start: 0.7139 (ttp80) cc_final: 0.6604 (ttp-110) REVERT: A 308 MET cc_start: 0.7001 (tpt) cc_final: 0.6754 (tpp) REVERT: A 376 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: A 418 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7021 (mt-10) REVERT: A 566 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.6999 (mtpt) REVERT: B 177 LYS cc_start: 0.7604 (pttt) cc_final: 0.7384 (mtmm) REVERT: B 196 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6634 (p90) REVERT: B 201 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 212 TYR cc_start: 0.7905 (t80) cc_final: 0.6247 (m-10) REVERT: B 239 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7056 (mtp85) REVERT: B 423 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7634 (t70) REVERT: B 436 LYS cc_start: 0.7400 (tttt) cc_final: 0.6911 (tttp) REVERT: B 439 LYS cc_start: 0.7865 (mttt) cc_final: 0.7602 (mtpp) REVERT: B 473 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.6171 (t0) REVERT: B 510 SER cc_start: 0.8851 (p) cc_final: 0.8472 (m) REVERT: B 541 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6731 (mpt-90) REVERT: B 570 GLU cc_start: 0.7229 (pp20) cc_final: 0.6705 (tm-30) outliers start: 35 outliers final: 18 residues processed: 144 average time/residue: 1.0541 time to fit residues: 159.7593 Evaluate side-chains 155 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 551 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2915 > 50: distance: 92 - 122: 16.390 distance: 99 - 133: 8.646 distance: 109 - 114: 6.314 distance: 110 - 141: 6.567 distance: 115 - 116: 6.204 distance: 115 - 118: 11.769 distance: 116 - 117: 4.887 distance: 117 - 149: 26.363 distance: 118 - 119: 14.550 distance: 118 - 120: 29.402 distance: 119 - 121: 26.968 distance: 122 - 123: 17.434 distance: 123 - 124: 14.713 distance: 123 - 126: 5.839 distance: 124 - 125: 11.996 distance: 124 - 133: 9.735 distance: 125 - 156: 13.810 distance: 126 - 127: 10.748 distance: 127 - 128: 10.609 distance: 128 - 129: 11.744 distance: 129 - 130: 10.856 distance: 130 - 131: 25.129 distance: 130 - 132: 13.943 distance: 133 - 134: 10.146 distance: 134 - 135: 12.772 distance: 134 - 137: 9.641 distance: 135 - 136: 8.710 distance: 135 - 141: 8.689 distance: 136 - 162: 38.486 distance: 137 - 138: 14.752 distance: 138 - 139: 12.025 distance: 138 - 140: 19.206 distance: 141 - 142: 9.367 distance: 142 - 143: 4.811 distance: 142 - 145: 11.876 distance: 143 - 144: 5.810 distance: 143 - 149: 16.922 distance: 144 - 170: 25.312 distance: 145 - 146: 9.444 distance: 146 - 148: 18.202 distance: 149 - 150: 15.586 distance: 150 - 151: 8.046 distance: 150 - 153: 15.449 distance: 151 - 152: 13.297 distance: 151 - 156: 6.549 distance: 152 - 178: 41.002 distance: 153 - 154: 5.900 distance: 153 - 155: 41.251 distance: 156 - 157: 39.563 distance: 157 - 158: 40.385 distance: 157 - 160: 11.697 distance: 158 - 159: 7.412 distance: 158 - 162: 42.820 distance: 160 - 161: 20.983 distance: 162 - 163: 24.430 distance: 163 - 164: 22.823 distance: 163 - 166: 5.627 distance: 164 - 165: 13.620 distance: 164 - 170: 19.537 distance: 166 - 167: 6.494 distance: 167 - 168: 9.772 distance: 167 - 169: 15.498 distance: 170 - 171: 12.993 distance: 171 - 172: 11.679 distance: 171 - 174: 34.858 distance: 172 - 173: 8.273 distance: 172 - 178: 14.825 distance: 174 - 175: 9.594 distance: 175 - 176: 28.001 distance: 176 - 177: 17.116 distance: 178 - 179: 15.354 distance: 179 - 180: 4.420 distance: 179 - 182: 20.283 distance: 180 - 181: 15.399 distance: 180 - 186: 21.235 distance: 182 - 183: 14.121 distance: 183 - 184: 13.078 distance: 183 - 185: 30.194 distance: 186 - 187: 9.020 distance: 187 - 188: 10.505 distance: 187 - 190: 12.888 distance: 188 - 189: 11.560 distance: 188 - 192: 11.071 distance: 190 - 191: 11.167