Starting phenix.real_space_refine on Fri Jun 6 15:20:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.map" model { file = "/net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf8_51311/06_2025/9gf8_51311.cif" } resolution = 3.5 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= 0.000 sd= 0.000 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 S 35 5.16 5 C 2562 2.51 5 N 648 2.21 5 O 683 1.98 5 H 3965 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7893 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6063 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 2 Chain: "B" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1830 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 4.29, per 1000 atoms: 0.54 Number of scatterers: 7893 At special positions: 0 Unit cell: (61.336, 87.516, 103.224, 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) S 35 16.00 O 683 8.00 N 648 7.00 C 2562 6.00 H 3965 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.80 Conformation dependent library (CDL) restraints added in 635.0 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 69.7% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 99 through 132 removed outlier: 4.179A pdb=" N VAL A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.855A pdb=" N ALA A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 144' Processing helix chain 'A' and resid 145 through 169 removed outlier: 3.896A pdb=" N MET A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.396A pdb=" N ILE A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 188 removed outlier: 3.943A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.640A pdb=" N GLN A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 3.516A pdb=" N VAL A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 258 through 277 removed outlier: 5.080A pdb=" N GLN A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 312 through 317 removed outlier: 4.209A pdb=" N VAL A 315 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.693A pdb=" N TRP A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.596A pdb=" N TYR A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.084A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 378 removed outlier: 3.807A pdb=" N LEU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 Processing helix chain 'A' and resid 386 through 404 removed outlier: 3.876A pdb=" N GLN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 429 removed outlier: 4.075A pdb=" N GLY A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 3.531A pdb=" N ILE A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 455 removed outlier: 3.666A pdb=" N MET A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 461 through 474 removed outlier: 4.091A pdb=" N ASN A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 4.085A pdb=" N TYR A 481 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.575A pdb=" N ILE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.625A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 25 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 84 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.675A pdb=" N HIS B 101 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET B 39 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA B 55 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP B 41 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14 238 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3953 1.03 - 1.23: 12 1.23 - 1.42: 1710 1.42 - 1.61: 2254 1.61 - 1.81: 58 Bond restraints: 7987 Sorted by residual: bond pdb=" N VAL B 4 " pdb=" CA VAL B 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N VAL B 4 " pdb=" H VAL B 4 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N GLY A 116 " pdb=" CA GLY A 116 " ideal model delta sigma weight residual 1.454 1.447 0.007 1.24e-02 6.50e+03 2.98e-01 bond pdb=" CA ILE A 404 " pdb=" CB ILE A 404 " ideal model delta sigma weight residual 1.539 1.536 0.003 5.40e-03 3.43e+04 2.86e-01 bond pdb=" CB PRO A 487 " pdb=" CG PRO A 487 " ideal model delta sigma weight residual 1.492 1.465 0.027 5.00e-02 4.00e+02 2.82e-01 ... (remaining 7982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 13525 1.05 - 2.10: 841 2.10 - 3.15: 16 3.15 - 4.20: 12 4.20 - 5.25: 4 Bond angle restraints: 14398 Sorted by residual: angle pdb=" CA VAL B 4 " pdb=" N VAL B 4 " pdb=" H VAL B 4 " ideal model delta sigma weight residual 114.00 109.48 4.52 3.00e+00 1.11e-01 2.27e+00 angle pdb=" CA TYR A 125 " pdb=" CB TYR A 125 " pdb=" CG TYR A 125 " ideal model delta sigma weight residual 113.90 111.32 2.58 1.80e+00 3.09e-01 2.05e+00 angle pdb=" C GLU A 349 " pdb=" CA GLU A 349 " pdb=" CB GLU A 349 " ideal model delta sigma weight residual 110.65 107.90 2.75 1.95e+00 2.63e-01 1.99e+00 angle pdb=" N GLU A 349 " pdb=" CA GLU A 349 " pdb=" CB GLU A 349 " ideal model delta sigma weight residual 113.65 111.72 1.93 1.47e+00 4.63e-01 1.73e+00 angle pdb=" C PRO A 486 " pdb=" N PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 125.00 130.25 -5.25 4.10e+00 5.95e-02 1.64e+00 ... (remaining 14393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3501 17.89 - 35.78: 156 35.78 - 53.68: 81 53.68 - 71.57: 26 71.57 - 89.46: 6 Dihedral angle restraints: 3770 sinusoidal: 2006 harmonic: 1764 Sorted by residual: dihedral pdb=" CA GLU A 348 " pdb=" C GLU A 348 " pdb=" N GLU A 349 " pdb=" CA GLU A 349 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" N GLU A 437 " pdb=" CA GLU A 437 " pdb=" CB GLU A 437 " pdb=" CG GLU A 437 " ideal model delta sinusoidal sigma weight residual -180.00 -122.13 -57.87 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG A 506 " pdb=" CB ARG A 506 " pdb=" CG ARG A 506 " pdb=" CD ARG A 506 " ideal model delta sinusoidal sigma weight residual 180.00 124.90 55.10 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 3767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 413 0.029 - 0.057: 128 0.057 - 0.086: 45 0.086 - 0.114: 20 0.114 - 0.143: 6 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA ILE A 353 " pdb=" N ILE A 353 " pdb=" C ILE A 353 " pdb=" CB ILE A 353 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL B 4 " pdb=" N VAL B 4 " pdb=" C VAL B 4 " pdb=" CB VAL B 4 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL A 497 " pdb=" N VAL A 497 " pdb=" C VAL A 497 " pdb=" CB VAL A 497 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 609 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 337 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.39e-01 pdb=" N PRO A 338 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 462 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.76e-01 pdb=" N PRO A 463 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 198 " -0.009 2.00e-02 2.50e+03 4.45e-03 5.94e-01 pdb=" CG TYR A 198 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 198 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 198 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 198 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 198 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 198 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 198 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 198 " -0.001 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 430 2.20 - 2.80: 16114 2.80 - 3.40: 21178 3.40 - 4.00: 26496 4.00 - 4.60: 41416 Nonbonded interactions: 105634 Sorted by model distance: nonbonded pdb=" H GLY B 17 " pdb=" O LEU B 90 " model vdw 1.605 2.450 nonbonded pdb=" H SER B 57 " pdb=" O ASN B 61 " model vdw 1.648 2.450 nonbonded pdb=" OE1 GLU B 8 " pdb=" H GLU B 8 " model vdw 1.659 2.450 nonbonded pdb=" OE2 GLU A 96 " pdb="HH11 ARG A 226 " model vdw 1.691 2.450 nonbonded pdb=" H LYS B 91 " pdb=" OD2 ASP B 94 " model vdw 1.702 2.450 ... (remaining 105629 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.260 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.340 Find NCS groups from input model: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 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 : 0.002 0.033 4022 Z= 0.099 Angle : 0.424 5.250 5442 Z= 0.229 Chirality : 0.036 0.143 612 Planarity : 0.003 0.023 682 Dihedral : 10.775 89.461 1424 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.96 % Allowed : 4.08 % Favored : 94.96 % 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: 0.32 (0.40), residues: 500 helix: 0.46 (0.32), residues: 290 sheet: -0.63 (0.71), residues: 49 loop : 0.36 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.002 0.001 HIS A 341 PHE 0.006 0.001 PHE A 182 TYR 0.012 0.001 TYR A 198 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.19948 ( 231) hydrogen bonds : angle 7.48418 ( 672) covalent geometry : bond 0.00204 ( 4022) covalent geometry : angle 0.42427 ( 5442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4064 (ttp) cc_final: 0.3821 (tmm) REVERT: A 210 SER cc_start: 0.8776 (t) cc_final: 0.8574 (t) REVERT: A 420 LEU cc_start: 0.8926 (tp) cc_final: 0.8647 (tt) REVERT: B 41 TRP cc_start: 0.3034 (m100) cc_final: 0.2471 (m100) outliers start: 4 outliers final: 2 residues processed: 134 average time/residue: 0.3686 time to fit residues: 59.9508 Evaluate side-chains 103 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 471 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.188274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137262 restraints weight = 16525.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143490 restraints weight = 6614.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147161 restraints weight = 4007.662| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4022 Z= 0.169 Angle : 0.549 5.423 5442 Z= 0.300 Chirality : 0.039 0.135 612 Planarity : 0.006 0.106 682 Dihedral : 5.250 52.163 554 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.92 % Allowed : 11.99 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.39), residues: 500 helix: 0.29 (0.31), residues: 301 sheet: -0.60 (0.71), residues: 49 loop : 0.16 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 41 HIS 0.003 0.001 HIS A 376 PHE 0.012 0.001 PHE A 224 TYR 0.014 0.001 TYR A 198 ARG 0.004 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.05545 ( 231) hydrogen bonds : angle 6.05959 ( 672) covalent geometry : bond 0.00356 ( 4022) covalent geometry : angle 0.54903 ( 5442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4189 (ttp) cc_final: 0.3830 (tmm) REVERT: A 264 GLN cc_start: 0.7929 (tt0) cc_final: 0.7720 (tp40) REVERT: B 102 VAL cc_start: 0.7196 (t) cc_final: 0.6982 (t) outliers start: 8 outliers final: 5 residues processed: 104 average time/residue: 0.3098 time to fit residues: 40.3476 Evaluate side-chains 99 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 49 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138294 restraints weight = 16707.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.144828 restraints weight = 6616.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148804 restraints weight = 3988.939| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4022 Z= 0.114 Angle : 0.496 5.286 5442 Z= 0.265 Chirality : 0.037 0.139 612 Planarity : 0.004 0.064 682 Dihedral : 5.134 51.701 554 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.40 % Allowed : 13.67 % Favored : 83.93 % 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: 0.31 (0.39), residues: 500 helix: 0.55 (0.31), residues: 301 sheet: -0.56 (0.72), residues: 47 loop : 0.08 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.002 0.001 HIS A 186 PHE 0.008 0.001 PHE A 182 TYR 0.013 0.001 TYR A 125 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 231) hydrogen bonds : angle 5.36292 ( 672) covalent geometry : bond 0.00242 ( 4022) covalent geometry : angle 0.49612 ( 5442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4009 (ttp) cc_final: 0.3703 (tmm) REVERT: B 25 THR cc_start: 0.5162 (m) cc_final: 0.4949 (p) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.2823 time to fit residues: 37.7747 Evaluate side-chains 100 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136160 restraints weight = 16747.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142463 restraints weight = 6701.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.146239 restraints weight = 4068.444| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4022 Z= 0.148 Angle : 0.509 5.364 5442 Z= 0.276 Chirality : 0.038 0.142 612 Planarity : 0.004 0.044 682 Dihedral : 5.165 51.266 554 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.36 % Allowed : 13.67 % Favored : 82.97 % 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: 0.21 (0.38), residues: 500 helix: 0.52 (0.30), residues: 301 sheet: -0.64 (0.71), residues: 47 loop : -0.09 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.003 0.001 HIS B 101 PHE 0.012 0.001 PHE A 224 TYR 0.014 0.001 TYR A 125 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 231) hydrogen bonds : angle 5.31754 ( 672) covalent geometry : bond 0.00324 ( 4022) covalent geometry : angle 0.50898 ( 5442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4048 (ttp) cc_final: 0.3718 (tmm) REVERT: A 270 MET cc_start: 0.7910 (mmt) cc_final: 0.7628 (mmp) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.3008 time to fit residues: 40.7962 Evaluate side-chains 105 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133995 restraints weight = 16780.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140394 restraints weight = 6839.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144200 restraints weight = 4192.951| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4022 Z= 0.136 Angle : 0.501 5.304 5442 Z= 0.272 Chirality : 0.037 0.142 612 Planarity : 0.004 0.052 682 Dihedral : 5.132 50.708 554 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.60 % Allowed : 13.91 % Favored : 82.49 % 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: 0.32 (0.38), residues: 500 helix: 0.67 (0.31), residues: 299 sheet: -0.69 (0.71), residues: 46 loop : -0.15 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.005 0.001 HIS A 341 PHE 0.011 0.001 PHE A 224 TYR 0.014 0.001 TYR A 125 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 231) hydrogen bonds : angle 5.12642 ( 672) covalent geometry : bond 0.00295 ( 4022) covalent geometry : angle 0.50134 ( 5442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4028 (ttp) cc_final: 0.3693 (tmm) REVERT: A 270 MET cc_start: 0.7910 (mmt) cc_final: 0.7656 (mmp) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2811 time to fit residues: 38.0514 Evaluate side-chains 105 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.190983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133917 restraints weight = 17431.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140677 restraints weight = 7134.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144569 restraints weight = 4413.590| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4022 Z= 0.123 Angle : 0.492 5.281 5442 Z= 0.265 Chirality : 0.037 0.141 612 Planarity : 0.004 0.047 682 Dihedral : 5.093 49.791 554 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.08 % Allowed : 14.39 % Favored : 81.53 % 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: 0.40 (0.39), residues: 500 helix: 0.78 (0.31), residues: 299 sheet: -0.73 (0.72), residues: 44 loop : -0.18 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 324 HIS 0.004 0.001 HIS A 341 PHE 0.012 0.001 PHE A 248 TYR 0.014 0.001 TYR A 125 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 231) hydrogen bonds : angle 4.96191 ( 672) covalent geometry : bond 0.00270 ( 4022) covalent geometry : angle 0.49246 ( 5442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.3918 (ttp) cc_final: 0.3581 (tmm) REVERT: A 270 MET cc_start: 0.7945 (mmt) cc_final: 0.7712 (mmp) outliers start: 17 outliers final: 16 residues processed: 107 average time/residue: 0.2734 time to fit residues: 38.0760 Evaluate side-chains 111 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 0.0670 chunk 28 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.188705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136605 restraints weight = 16984.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142986 restraints weight = 6768.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.146799 restraints weight = 4088.573| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4022 Z= 0.121 Angle : 0.488 5.274 5442 Z= 0.262 Chirality : 0.037 0.142 612 Planarity : 0.004 0.046 682 Dihedral : 5.044 48.031 554 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.84 % Allowed : 15.35 % Favored : 80.82 % 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: 0.45 (0.39), residues: 500 helix: 0.83 (0.31), residues: 299 sheet: -0.75 (0.72), residues: 44 loop : -0.21 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 41 HIS 0.003 0.001 HIS A 477 PHE 0.009 0.001 PHE A 224 TYR 0.014 0.001 TYR A 125 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 231) hydrogen bonds : angle 4.87830 ( 672) covalent geometry : bond 0.00267 ( 4022) covalent geometry : angle 0.48773 ( 5442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4030 (ttp) cc_final: 0.3678 (tmm) REVERT: A 270 MET cc_start: 0.7947 (mmt) cc_final: 0.7720 (mmp) REVERT: A 477 HIS cc_start: 0.6230 (t-90) cc_final: 0.5762 (t70) outliers start: 16 outliers final: 15 residues processed: 106 average time/residue: 0.2637 time to fit residues: 36.2880 Evaluate side-chains 110 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.186952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133900 restraints weight = 17049.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140283 restraints weight = 6861.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144148 restraints weight = 4172.817| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4022 Z= 0.163 Angle : 0.527 5.316 5442 Z= 0.288 Chirality : 0.038 0.139 612 Planarity : 0.004 0.049 682 Dihedral : 5.155 48.190 554 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.56 % Allowed : 14.87 % Favored : 80.58 % 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: 0.27 (0.38), residues: 500 helix: 0.74 (0.31), residues: 299 sheet: -0.74 (0.71), residues: 44 loop : -0.41 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 41 HIS 0.003 0.001 HIS A 477 PHE 0.014 0.001 PHE A 224 TYR 0.015 0.002 TYR A 125 ARG 0.003 0.000 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 231) hydrogen bonds : angle 5.02611 ( 672) covalent geometry : bond 0.00356 ( 4022) covalent geometry : angle 0.52729 ( 5442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4057 (ttp) cc_final: 0.3698 (tmm) REVERT: A 270 MET cc_start: 0.7913 (mmt) cc_final: 0.7678 (mmp) REVERT: A 477 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5793 (t70) REVERT: B 101 HIS cc_start: 0.7238 (t70) cc_final: 0.6982 (t-90) outliers start: 19 outliers final: 18 residues processed: 105 average time/residue: 0.2576 time to fit residues: 35.4020 Evaluate side-chains 112 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134871 restraints weight = 17255.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141253 restraints weight = 6821.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145178 restraints weight = 4138.008| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4022 Z= 0.135 Angle : 0.511 5.245 5442 Z= 0.277 Chirality : 0.037 0.139 612 Planarity : 0.004 0.035 682 Dihedral : 5.211 47.750 554 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.56 % Allowed : 15.35 % Favored : 80.10 % 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: 0.31 (0.38), residues: 500 helix: 0.78 (0.31), residues: 298 sheet: -0.72 (0.71), residues: 44 loop : -0.42 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 324 HIS 0.006 0.001 HIS A 477 PHE 0.011 0.001 PHE A 336 TYR 0.015 0.002 TYR A 125 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 231) hydrogen bonds : angle 4.91024 ( 672) covalent geometry : bond 0.00295 ( 4022) covalent geometry : angle 0.51095 ( 5442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4041 (ttp) cc_final: 0.3682 (tmm) REVERT: A 270 MET cc_start: 0.7911 (mmt) cc_final: 0.7677 (mmp) REVERT: A 477 HIS cc_start: 0.6613 (t-90) cc_final: 0.6413 (t70) outliers start: 19 outliers final: 17 residues processed: 106 average time/residue: 0.2627 time to fit residues: 36.4235 Evaluate side-chains 109 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.187918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135027 restraints weight = 16912.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141407 restraints weight = 6725.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145236 restraints weight = 4084.730| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4022 Z= 0.122 Angle : 0.502 5.685 5442 Z= 0.270 Chirality : 0.037 0.141 612 Planarity : 0.004 0.036 682 Dihedral : 5.118 47.672 554 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.84 % Allowed : 15.83 % Favored : 80.34 % 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: 0.46 (0.39), residues: 500 helix: 0.88 (0.31), residues: 299 sheet: -0.53 (0.73), residues: 44 loop : -0.37 (0.53), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 324 HIS 0.003 0.001 HIS A 477 PHE 0.009 0.001 PHE A 224 TYR 0.014 0.001 TYR A 125 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 231) hydrogen bonds : angle 4.80508 ( 672) covalent geometry : bond 0.00270 ( 4022) covalent geometry : angle 0.50162 ( 5442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4072 (ttp) cc_final: 0.3701 (tmm) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.2599 time to fit residues: 35.2715 Evaluate side-chains 108 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.186248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.133080 restraints weight = 17171.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139392 restraints weight = 6837.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.143201 restraints weight = 4159.778| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4022 Z= 0.158 Angle : 0.526 5.277 5442 Z= 0.286 Chirality : 0.038 0.138 612 Planarity : 0.004 0.039 682 Dihedral : 5.205 48.987 554 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.08 % Allowed : 15.35 % Favored : 80.58 % 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: 0.32 (0.38), residues: 500 helix: 0.78 (0.31), residues: 298 sheet: -0.51 (0.73), residues: 44 loop : -0.46 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.002 0.001 HIS A 376 PHE 0.013 0.001 PHE A 224 TYR 0.016 0.002 TYR A 125 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 231) hydrogen bonds : angle 4.95061 ( 672) covalent geometry : bond 0.00347 ( 4022) covalent geometry : angle 0.52624 ( 5442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.22 seconds wall clock time: 62 minutes 12.29 seconds (3732.29 seconds total)