Starting phenix.real_space_refine on Tue Jul 29 08:38:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.map" model { file = "/net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c8d_30305/07_2025/7c8d_30305.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4074 2.51 5 N 1058 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4815 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 568} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.73 Number of scatterers: 6359 At special positions: 0 Unit cell: (96.3937, 93.4125, 107.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1190 8.00 N 1058 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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: 1.92 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 53.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.692A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.551A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.278A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 3.575A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.665A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.512A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.212A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.704A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.577A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.750A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.605A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.549A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.814A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.503A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.435A pdb=" N LYS A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.843A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.512A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.212A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.784A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 290 hydrogen bonds defined for protein. 822 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: 2.29 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2037 1.35 - 1.48: 1777 1.48 - 1.61: 2669 1.61 - 1.73: 0 1.73 - 1.86: 56 Bond restraints: 6539 Sorted by residual: bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.862 -0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.23e-02 6.61e+03 9.96e-01 bond pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.48e-02 4.57e+03 7.81e-01 bond pdb=" CA ASP B 364 " pdb=" C ASP B 364 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 7.57e-01 bond pdb=" CA TYR A 83 " pdb=" CB TYR A 83 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.68e-02 3.54e+03 6.57e-01 ... (remaining 6534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8727 1.56 - 3.12: 134 3.12 - 4.68: 18 4.68 - 6.24: 9 6.24 - 7.80: 1 Bond angle restraints: 8889 Sorted by residual: angle pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 114.93 -5.12 2.21e+00 2.05e-01 5.36e+00 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.06e+00 angle pdb=" CA LEU B 335 " pdb=" CB LEU B 335 " pdb=" CG LEU B 335 " ideal model delta sigma weight residual 116.30 124.10 -7.80 3.50e+00 8.16e-02 4.97e+00 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.60 111.76 -3.16 1.46e+00 4.69e-01 4.69e+00 ... (remaining 8884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3364 17.84 - 35.68: 356 35.68 - 53.52: 102 53.52 - 71.36: 20 71.36 - 89.20: 21 Dihedral angle restraints: 3863 sinusoidal: 1540 harmonic: 2323 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -33.10 -52.90 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -37.81 -48.19 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA THR B 500 " pdb=" C THR B 500 " pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 551 0.031 - 0.061: 280 0.061 - 0.092: 65 0.092 - 0.122: 38 0.122 - 0.153: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 283 " pdb=" N VAL A 283 " pdb=" C VAL A 283 " pdb=" CB VAL A 283 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ASN B 501 " pdb=" N ASN B 501 " pdb=" C ASN B 501 " pdb=" CB ASN B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 933 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 384 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 235 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 490 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.016 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 68 2.58 - 3.16: 5111 3.16 - 3.74: 10330 3.74 - 4.32: 14653 4.32 - 4.90: 23826 Nonbonded interactions: 53988 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 801 " model vdw 1.998 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.188 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.217 3.040 ... (remaining 53983 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 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: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.720 Find NCS groups from input model: 0.060 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:25.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 6548 Z= 0.182 Angle : 0.537 7.804 8903 Z= 0.303 Chirality : 0.040 0.153 936 Planarity : 0.004 0.036 1146 Dihedral : 17.372 89.203 2352 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.05 % Allowed : 20.21 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.26), residues: 788 helix: -1.60 (0.23), residues: 390 sheet: -0.38 (0.88), residues: 36 loop : -2.25 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE A 308 TYR 0.010 0.001 TYR A 385 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.17411 ( 290) hydrogen bonds : angle 6.87241 ( 822) metal coordination : bond 0.20170 ( 2) SS BOND : bond 0.00827 ( 7) SS BOND : angle 2.03517 ( 14) covalent geometry : bond 0.00289 ( 6539) covalent geometry : angle 0.53112 ( 8889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.744 Fit side-chains REVERT: A 62 MET cc_start: 0.7469 (ttt) cc_final: 0.7189 (ttp) REVERT: A 363 LYS cc_start: 0.6862 (mmtp) cc_final: 0.6277 (mttp) REVERT: A 510 TYR cc_start: 0.8058 (m-80) cc_final: 0.7855 (m-80) REVERT: A 579 MET cc_start: 0.8197 (ttm) cc_final: 0.7966 (ttm) outliers start: 41 outliers final: 11 residues processed: 160 average time/residue: 1.1819 time to fit residues: 198.9859 Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 290 ASN A 345 HIS A 416 ASN A 598 GLN B 354 ASN B 360 ASN B 501 ASN B 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134020 restraints weight = 8726.540| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.08 r_work: 0.3506 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6548 Z= 0.144 Angle : 0.567 14.900 8903 Z= 0.295 Chirality : 0.042 0.215 936 Planarity : 0.004 0.043 1146 Dihedral : 5.676 57.858 876 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.98 % Allowed : 23.75 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.51 (0.29), residues: 788 helix: -0.41 (0.26), residues: 396 sheet: -0.23 (0.92), residues: 36 loop : -1.73 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 308 TYR 0.016 0.002 TYR B 351 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 290) hydrogen bonds : angle 4.79529 ( 822) metal coordination : bond 0.00477 ( 2) SS BOND : bond 0.00999 ( 7) SS BOND : angle 2.10455 ( 14) covalent geometry : bond 0.00331 ( 6539) covalent geometry : angle 0.56085 ( 8889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.718 Fit side-chains REVERT: A 62 MET cc_start: 0.7696 (ttt) cc_final: 0.7413 (ttp) REVERT: A 287 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6559 (pp30) REVERT: A 363 LYS cc_start: 0.6830 (mmtp) cc_final: 0.6306 (mttp) REVERT: A 503 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 603 PHE cc_start: 0.6657 (t80) cc_final: 0.6242 (t80) REVERT: B 493 GLN cc_start: 0.5943 (tm-30) cc_final: 0.5713 (tm130) REVERT: B 515 PHE cc_start: 0.6215 (m-80) cc_final: 0.5932 (m-80) outliers start: 27 outliers final: 11 residues processed: 128 average time/residue: 0.9730 time to fit residues: 132.3023 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128706 restraints weight = 8811.589| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.05 r_work: 0.3428 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6548 Z= 0.210 Angle : 0.614 14.369 8903 Z= 0.319 Chirality : 0.044 0.178 936 Planarity : 0.005 0.055 1146 Dihedral : 5.922 57.660 868 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.31 % Allowed : 23.45 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.25 (0.29), residues: 788 helix: -0.18 (0.26), residues: 393 sheet: -0.21 (0.96), residues: 36 loop : -1.59 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.002 PHE A 308 TYR 0.015 0.002 TYR A 516 ARG 0.005 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 290) hydrogen bonds : angle 4.85174 ( 822) metal coordination : bond 0.00262 ( 2) SS BOND : bond 0.00874 ( 7) SS BOND : angle 1.81018 ( 14) covalent geometry : bond 0.00489 ( 6539) covalent geometry : angle 0.61014 ( 8889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: A 363 LYS cc_start: 0.6937 (mmtp) cc_final: 0.6306 (mttp) REVERT: A 503 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 603 PHE cc_start: 0.6639 (t80) cc_final: 0.6274 (t80) REVERT: B 501 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7639 (t0) REVERT: B 515 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5983 (m-80) outliers start: 36 outliers final: 21 residues processed: 128 average time/residue: 0.9187 time to fit residues: 125.5024 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 598 GLN B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130866 restraints weight = 8877.896| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.06 r_work: 0.3459 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6548 Z= 0.151 Angle : 0.562 14.097 8903 Z= 0.290 Chirality : 0.042 0.170 936 Planarity : 0.004 0.041 1146 Dihedral : 5.777 58.508 868 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.49 % Allowed : 21.68 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.30), residues: 788 helix: 0.13 (0.26), residues: 394 sheet: -0.65 (0.81), residues: 46 loop : -1.35 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 315 TYR 0.013 0.002 TYR A 516 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 290) hydrogen bonds : angle 4.64351 ( 822) metal coordination : bond 0.00159 ( 2) SS BOND : bond 0.00929 ( 7) SS BOND : angle 1.78856 ( 14) covalent geometry : bond 0.00350 ( 6539) covalent geometry : angle 0.55829 ( 8889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7847 (t70) cc_final: 0.7472 (t0) REVERT: A 208 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: A 287 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6600 (pp30) REVERT: A 306 ARG cc_start: 0.6937 (tpt-90) cc_final: 0.6487 (ttt180) REVERT: A 478 TRP cc_start: 0.8013 (m100) cc_final: 0.7702 (m100) REVERT: A 503 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 603 PHE cc_start: 0.6576 (t80) cc_final: 0.6246 (t80) REVERT: B 501 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7583 (t0) REVERT: B 515 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5750 (m-80) outliers start: 44 outliers final: 20 residues processed: 138 average time/residue: 1.0005 time to fit residues: 146.4338 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 73 optimal weight: 0.0770 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS A 598 GLN B 493 GLN B 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.160764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133978 restraints weight = 8645.589| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.01 r_work: 0.3500 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6548 Z= 0.125 Angle : 0.580 17.772 8903 Z= 0.296 Chirality : 0.041 0.184 936 Planarity : 0.004 0.035 1146 Dihedral : 5.660 58.427 867 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.31 % Allowed : 23.16 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.60 (0.30), residues: 788 helix: 0.39 (0.27), residues: 393 sheet: -0.59 (0.81), residues: 46 loop : -1.25 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE B 429 TYR 0.012 0.001 TYR A 516 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 290) hydrogen bonds : angle 4.60390 ( 822) metal coordination : bond 0.00106 ( 2) SS BOND : bond 0.00795 ( 7) SS BOND : angle 2.93583 ( 14) covalent geometry : bond 0.00279 ( 6539) covalent geometry : angle 0.56877 ( 8889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7832 (t70) cc_final: 0.7473 (t0) REVERT: A 160 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: A 208 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: A 287 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6547 (pp30) REVERT: A 306 ARG cc_start: 0.6965 (tpt-90) cc_final: 0.6548 (ttt180) REVERT: A 478 TRP cc_start: 0.7984 (m100) cc_final: 0.7639 (m100) REVERT: A 510 TYR cc_start: 0.8332 (m-80) cc_final: 0.8112 (m-80) REVERT: A 603 PHE cc_start: 0.6572 (t80) cc_final: 0.6263 (t80) REVERT: B 396 TYR cc_start: 0.6944 (m-80) cc_final: 0.6703 (m-80) REVERT: B 501 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7601 (t0) REVERT: B 515 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5811 (m-80) outliers start: 36 outliers final: 17 residues processed: 128 average time/residue: 1.0350 time to fit residues: 140.9677 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 139 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 24 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134344 restraints weight = 8679.278| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.04 r_work: 0.3501 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6548 Z= 0.113 Angle : 0.576 17.628 8903 Z= 0.294 Chirality : 0.041 0.179 936 Planarity : 0.004 0.035 1146 Dihedral : 5.305 58.780 867 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.72 % Allowed : 23.45 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.38 (0.30), residues: 788 helix: 0.59 (0.27), residues: 393 sheet: -0.53 (0.78), residues: 48 loop : -1.15 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE B 429 TYR 0.014 0.001 TYR A 183 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 290) hydrogen bonds : angle 4.53136 ( 822) metal coordination : bond 0.00071 ( 2) SS BOND : bond 0.00597 ( 7) SS BOND : angle 3.03636 ( 14) covalent geometry : bond 0.00247 ( 6539) covalent geometry : angle 0.56417 ( 8889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.702 Fit side-chains REVERT: A 157 ASP cc_start: 0.7868 (t70) cc_final: 0.7551 (t0) REVERT: A 287 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6491 (pp30) REVERT: A 465 LYS cc_start: 0.8157 (mttt) cc_final: 0.7650 (mtpt) REVERT: A 478 TRP cc_start: 0.7961 (m100) cc_final: 0.7579 (m100) REVERT: A 516 TYR cc_start: 0.8546 (t80) cc_final: 0.7889 (t80) REVERT: B 421 TYR cc_start: 0.8150 (m-10) cc_final: 0.7866 (m-10) REVERT: B 458 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7427 (mtpt) REVERT: B 501 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 515 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: B 516 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.4609 (pp20) outliers start: 32 outliers final: 16 residues processed: 123 average time/residue: 0.9728 time to fit residues: 127.0442 Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133464 restraints weight = 8754.454| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.06 r_work: 0.3501 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6548 Z= 0.123 Angle : 0.579 17.716 8903 Z= 0.297 Chirality : 0.041 0.174 936 Planarity : 0.004 0.035 1146 Dihedral : 5.271 57.986 867 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.16 % Allowed : 24.19 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.33 (0.30), residues: 788 helix: 0.64 (0.27), residues: 393 sheet: -0.64 (0.77), residues: 48 loop : -1.12 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE A 308 TYR 0.021 0.002 TYR B 351 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 290) hydrogen bonds : angle 4.53168 ( 822) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00683 ( 7) SS BOND : angle 3.09557 ( 14) covalent geometry : bond 0.00277 ( 6539) covalent geometry : angle 0.56644 ( 8889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7875 (t70) cc_final: 0.7600 (t0) REVERT: A 208 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: A 287 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6434 (pp30) REVERT: A 478 TRP cc_start: 0.7946 (m100) cc_final: 0.7594 (m100) REVERT: B 355 ARG cc_start: 0.7482 (ttm170) cc_final: 0.7219 (ttm170) REVERT: B 421 TYR cc_start: 0.8163 (m-10) cc_final: 0.7776 (m-10) REVERT: B 458 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7369 (mtpt) REVERT: B 501 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7456 (t0) REVERT: B 515 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5650 (m-80) outliers start: 35 outliers final: 19 residues processed: 121 average time/residue: 0.9575 time to fit residues: 123.0048 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.0070 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 450 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.164164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136260 restraints weight = 8688.005| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.07 r_work: 0.3526 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6548 Z= 0.105 Angle : 0.597 16.039 8903 Z= 0.306 Chirality : 0.040 0.165 936 Planarity : 0.004 0.035 1146 Dihedral : 5.086 58.175 867 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.72 % Allowed : 25.07 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.09 (0.30), residues: 788 helix: 0.85 (0.27), residues: 391 sheet: -0.23 (0.87), residues: 38 loop : -1.04 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 302 HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE A 315 TYR 0.021 0.001 TYR B 351 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 290) hydrogen bonds : angle 4.63127 ( 822) metal coordination : bond 0.00041 ( 2) SS BOND : bond 0.00451 ( 7) SS BOND : angle 4.46015 ( 14) covalent geometry : bond 0.00221 ( 6539) covalent geometry : angle 0.57100 ( 8889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6437 (pp30) REVERT: A 343 VAL cc_start: 0.5628 (OUTLIER) cc_final: 0.5163 (m) REVERT: A 465 LYS cc_start: 0.8094 (mttt) cc_final: 0.7626 (mtpt) REVERT: A 478 TRP cc_start: 0.7943 (m100) cc_final: 0.7625 (m100) REVERT: A 510 TYR cc_start: 0.8231 (m-80) cc_final: 0.8026 (m-80) REVERT: A 516 TYR cc_start: 0.8531 (t80) cc_final: 0.7932 (t80) REVERT: A 598 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6093 (tm-30) REVERT: B 355 ARG cc_start: 0.7501 (ttm170) cc_final: 0.7196 (ttm170) REVERT: B 406 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 421 TYR cc_start: 0.8106 (m-10) cc_final: 0.7694 (m-10) REVERT: B 501 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7325 (t0) REVERT: B 515 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5632 (m-80) outliers start: 32 outliers final: 15 residues processed: 121 average time/residue: 1.1709 time to fit residues: 150.1319 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134341 restraints weight = 8688.379| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.04 r_work: 0.3515 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.120 Angle : 0.693 26.857 8903 Z= 0.346 Chirality : 0.042 0.289 936 Planarity : 0.004 0.036 1146 Dihedral : 4.911 58.350 866 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.57 % Allowed : 25.81 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.02 (0.31), residues: 788 helix: 0.84 (0.27), residues: 393 sheet: 0.14 (0.91), residues: 36 loop : -0.96 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 302 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 315 TYR 0.019 0.002 TYR B 351 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 290) hydrogen bonds : angle 4.44047 ( 822) metal coordination : bond 0.00093 ( 2) SS BOND : bond 0.01024 ( 7) SS BOND : angle 5.05289 ( 14) covalent geometry : bond 0.00262 ( 6539) covalent geometry : angle 0.66382 ( 8889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: A 343 VAL cc_start: 0.5659 (OUTLIER) cc_final: 0.5082 (m) REVERT: A 465 LYS cc_start: 0.8116 (mttt) cc_final: 0.7632 (mtpt) REVERT: A 478 TRP cc_start: 0.7897 (m100) cc_final: 0.7529 (m100) REVERT: A 503 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 516 TYR cc_start: 0.8583 (t80) cc_final: 0.7779 (t80) REVERT: A 598 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6276 (tm-30) REVERT: B 355 ARG cc_start: 0.7433 (ttm170) cc_final: 0.7156 (ttm170) REVERT: B 421 TYR cc_start: 0.8074 (m-10) cc_final: 0.7595 (m-10) REVERT: B 501 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7428 (t0) outliers start: 31 outliers final: 17 residues processed: 121 average time/residue: 1.6198 time to fit residues: 207.7154 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134556 restraints weight = 8754.133| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.04 r_work: 0.3514 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.123 Angle : 0.663 25.782 8903 Z= 0.337 Chirality : 0.043 0.346 936 Planarity : 0.004 0.037 1146 Dihedral : 4.885 58.552 866 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.83 % Allowed : 26.70 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.00 (0.30), residues: 788 helix: 0.82 (0.27), residues: 395 sheet: 0.53 (0.90), residues: 36 loop : -0.96 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 302 HIS 0.002 0.001 HIS A 241 PHE 0.007 0.001 PHE A 452 TYR 0.020 0.002 TYR A 50 ARG 0.004 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 290) hydrogen bonds : angle 4.26836 ( 822) metal coordination : bond 0.00082 ( 2) SS BOND : bond 0.01105 ( 7) SS BOND : angle 4.87657 ( 14) covalent geometry : bond 0.00267 ( 6539) covalent geometry : angle 0.63486 ( 8889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: A 343 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5041 (m) REVERT: A 478 TRP cc_start: 0.7928 (m100) cc_final: 0.7547 (m100) REVERT: A 503 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 516 TYR cc_start: 0.8564 (t80) cc_final: 0.7825 (t80) REVERT: A 598 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: B 355 ARG cc_start: 0.7333 (ttm170) cc_final: 0.7042 (ttt90) REVERT: B 421 TYR cc_start: 0.8102 (m-10) cc_final: 0.7627 (m-10) REVERT: B 501 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7406 (t0) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 1.3556 time to fit residues: 159.1990 Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133421 restraints weight = 8903.228| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.05 r_work: 0.3496 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.129 Angle : 0.680 23.527 8903 Z= 0.342 Chirality : 0.042 0.259 936 Planarity : 0.004 0.037 1146 Dihedral : 5.008 58.604 866 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.83 % Allowed : 26.70 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.04 (0.31), residues: 788 helix: 0.82 (0.27), residues: 393 sheet: 0.27 (0.94), residues: 36 loop : -1.00 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 302 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 315 TYR 0.021 0.002 TYR A 50 ARG 0.004 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 290) hydrogen bonds : angle 4.50305 ( 822) metal coordination : bond 0.00116 ( 2) SS BOND : bond 0.00774 ( 7) SS BOND : angle 5.15547 ( 14) covalent geometry : bond 0.00287 ( 6539) covalent geometry : angle 0.64948 ( 8889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5824.32 seconds wall clock time: 105 minutes 23.29 seconds (6323.29 seconds total)