Starting phenix.real_space_refine on Sat May 10 04:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy1_46004/05_2025/9cy1_46004.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 3286 2.51 5 N 812 2.21 5 O 889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5026 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4114 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 6 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.12, per 1000 atoms: 0.82 Number of scatterers: 5026 At special positions: 0 Unit cell: (61.544, 103.306, 103.306, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 889 8.00 N 812 7.00 C 3286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.04 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " 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: 1.29 Conformation dependent library (CDL) restraints added in 753.6 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 57.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 62 through 88 removed outlier: 4.323A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.519A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.883A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.789A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.615A pdb=" N PHE A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.732A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.756A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 335 through 367 removed outlier: 3.991A pdb=" N TYR A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 401 Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.647A pdb=" N ASN A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 461 " --> pdb=" O TYR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 461' Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.725A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 4.241A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 583 removed outlier: 3.628A pdb=" N HIS A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.720A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 removed outlier: 3.733A pdb=" N SER A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 removed outlier: 5.759A pdb=" N CYS A 489 " --> pdb=" O CYS A 504 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS A 504 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.857A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP A 602 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N CYS A 613 " --> pdb=" O TRP A 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 removed outlier: 6.792A pdb=" N VAL B 16 " --> pdb=" O SER B 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.587A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.587A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 113 " --> pdb=" O TYR B 98 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1481 1.34 - 1.46: 1294 1.46 - 1.58: 2319 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5152 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N PRO A 190 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.18e+00 bond pdb=" C ARG A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.33e+00 bond pdb=" C ILE A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.10e+00 bond pdb=" CB THR A 186 " pdb=" CG2 THR A 186 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.43e+00 bond pdb=" C LEU A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.19e+00 ... (remaining 5147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 6851 2.95 - 5.90: 101 5.90 - 8.85: 20 8.85 - 11.80: 0 11.80 - 14.75: 1 Bond angle restraints: 6973 Sorted by residual: angle pdb=" N VAL B 33 " pdb=" CA VAL B 33 " pdb=" C VAL B 33 " ideal model delta sigma weight residual 111.91 107.73 4.18 8.90e-01 1.26e+00 2.20e+01 angle pdb=" C ASP A 197 " pdb=" CA ASP A 197 " pdb=" CB ASP A 197 " ideal model delta sigma weight residual 109.72 118.38 -8.66 1.92e+00 2.71e-01 2.03e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 131.05 -14.75 3.50e+00 8.16e-02 1.78e+01 angle pdb=" C ALA B 18 " pdb=" CA ALA B 18 " pdb=" CB ALA B 18 " ideal model delta sigma weight residual 115.89 110.42 5.47 1.32e+00 5.74e-01 1.72e+01 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 121.18 -7.28 1.80e+00 3.09e-01 1.64e+01 ... (remaining 6968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 2658 16.09 - 32.17: 265 32.17 - 48.25: 55 48.25 - 64.34: 6 64.34 - 80.42: 5 Dihedral angle restraints: 2989 sinusoidal: 1136 harmonic: 1853 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -35.14 -50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 2986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 633 0.062 - 0.124: 124 0.124 - 0.187: 18 0.187 - 0.249: 4 0.249 - 0.311: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" CB ILE A 47 " pdb=" CA ILE A 47 " pdb=" CG1 ILE A 47 " pdb=" CG2 ILE A 47 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA PHE A 117 " pdb=" N PHE A 117 " pdb=" C PHE A 117 " pdb=" CB PHE A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 66 " pdb=" CA VAL A 66 " pdb=" CG1 VAL A 66 " pdb=" CG2 VAL A 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 778 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 113 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 114 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " 0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A 283 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 115 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C VAL B 115 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL B 115 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 116 " -0.015 2.00e-02 2.50e+03 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1279 2.80 - 3.32: 4534 3.32 - 3.85: 8317 3.85 - 4.37: 9622 4.37 - 4.90: 16918 Nonbonded interactions: 40670 Sorted by model distance: nonbonded pdb=" OH TYR A 425 " pdb=" OE1 GLN A 541 " model vdw 2.269 3.040 nonbonded pdb=" O ASN B 34 " pdb=" OG SER B 57 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLN A 348 " pdb=" OH TYR A 640 " model vdw 2.317 3.040 nonbonded pdb=" O LEU A 346 " pdb=" OG SER A 350 " model vdw 2.331 3.040 nonbonded pdb=" OE1 GLN A 365 " pdb=" NZ LYS A 433 " model vdw 2.350 3.120 ... (remaining 40665 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 0.058 5159 Z= 0.233 Angle : 0.911 14.749 6987 Z= 0.490 Chirality : 0.054 0.311 781 Planarity : 0.008 0.105 858 Dihedral : 13.400 80.423 1792 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.80 (0.30), residues: 633 helix: -0.25 (0.25), residues: 324 sheet: -0.61 (0.67), residues: 63 loop : -0.68 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 602 HIS 0.006 0.001 HIS A 115 PHE 0.040 0.002 PHE A 386 TYR 0.033 0.002 TYR A 590 ARG 0.012 0.001 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.13698 ( 295) hydrogen bonds : angle 7.09302 ( 879) SS BOND : bond 0.00379 ( 7) SS BOND : angle 1.23131 ( 14) covalent geometry : bond 0.00518 ( 5152) covalent geometry : angle 0.90976 ( 6973) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.573 Fit side-chains REVERT: A 348 GLN cc_start: 0.7589 (tp40) cc_final: 0.7234 (tt0) REVERT: A 417 MET cc_start: 0.7379 (tpp) cc_final: 0.7113 (tpp) REVERT: A 557 MET cc_start: 0.7598 (mmp) cc_final: 0.7231 (mmp) REVERT: A 577 MET cc_start: 0.7272 (ttt) cc_final: 0.7016 (ttp) REVERT: A 649 LYS cc_start: 0.7703 (tptm) cc_final: 0.7496 (tttt) REVERT: B 58 TRP cc_start: 0.6691 (m100) cc_final: 0.6166 (m-10) REVERT: B 108 TYR cc_start: 0.7153 (m-10) cc_final: 0.6912 (m-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1474 time to fit residues: 23.6289 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 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 477 ASN B 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.173384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136255 restraints weight = 5598.094| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.03 r_work: 0.3469 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5159 Z= 0.144 Angle : 0.536 5.378 6987 Z= 0.288 Chirality : 0.041 0.141 781 Planarity : 0.005 0.077 858 Dihedral : 4.145 20.575 699 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.20 % Allowed : 7.89 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.32), residues: 633 helix: 1.18 (0.27), residues: 332 sheet: -0.19 (0.80), residues: 46 loop : -0.37 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.003 0.001 HIS B 61 PHE 0.022 0.002 PHE A 386 TYR 0.026 0.002 TYR A 590 ARG 0.003 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 295) hydrogen bonds : angle 4.73058 ( 879) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.93374 ( 14) covalent geometry : bond 0.00328 ( 5152) covalent geometry : angle 0.53449 ( 6973) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.573 Fit side-chains REVERT: A 25 ASN cc_start: 0.7357 (t0) cc_final: 0.7134 (t0) REVERT: A 46 ILE cc_start: 0.8537 (tp) cc_final: 0.8280 (tp) REVERT: A 70 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: A 90 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8198 (mmtm) REVERT: A 348 GLN cc_start: 0.7834 (tp40) cc_final: 0.7438 (tt0) REVERT: A 557 MET cc_start: 0.8130 (mmp) cc_final: 0.7694 (mmp) REVERT: A 577 MET cc_start: 0.8182 (ttt) cc_final: 0.7924 (ttp) REVERT: A 645 TYR cc_start: 0.7886 (t80) cc_final: 0.7189 (t80) REVERT: A 649 LYS cc_start: 0.7902 (tptm) cc_final: 0.7425 (tttt) REVERT: B 58 TRP cc_start: 0.7011 (m100) cc_final: 0.6136 (m-10) REVERT: B 87 MET cc_start: 0.7910 (mtp) cc_final: 0.7475 (mtm) REVERT: B 108 TYR cc_start: 0.8001 (m-10) cc_final: 0.7632 (m-80) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 0.1479 time to fit residues: 21.1122 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134359 restraints weight = 5669.887| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.05 r_work: 0.3455 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5159 Z= 0.138 Angle : 0.509 5.579 6987 Z= 0.272 Chirality : 0.041 0.219 781 Planarity : 0.004 0.059 858 Dihedral : 3.885 19.788 699 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 10.09 % Favored : 87.34 % 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: 1.11 (0.33), residues: 633 helix: 1.66 (0.28), residues: 333 sheet: 0.04 (0.83), residues: 46 loop : -0.31 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.015 0.001 PHE A 117 TYR 0.026 0.001 TYR A 590 ARG 0.002 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 295) hydrogen bonds : angle 4.41863 ( 879) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.79674 ( 14) covalent geometry : bond 0.00323 ( 5152) covalent geometry : angle 0.50850 ( 6973) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.802 Fit side-chains REVERT: A 25 ASN cc_start: 0.7234 (t0) cc_final: 0.7010 (t0) REVERT: A 46 ILE cc_start: 0.8584 (tp) cc_final: 0.8343 (tp) REVERT: A 47 ILE cc_start: 0.8725 (mm) cc_final: 0.8464 (mm) REVERT: A 60 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8027 (mm-30) REVERT: A 70 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: A 173 TYR cc_start: 0.7722 (m-10) cc_final: 0.7489 (m-80) REVERT: A 348 GLN cc_start: 0.7778 (tp40) cc_final: 0.7361 (tt0) REVERT: A 477 ASN cc_start: 0.7317 (m110) cc_final: 0.7053 (m110) REVERT: A 557 MET cc_start: 0.8103 (mmp) cc_final: 0.7661 (mmt) REVERT: A 645 TYR cc_start: 0.7933 (t80) cc_final: 0.7196 (t80) REVERT: A 649 LYS cc_start: 0.7870 (tptm) cc_final: 0.7498 (tttm) REVERT: B 58 TRP cc_start: 0.7044 (m100) cc_final: 0.6103 (m-10) REVERT: B 87 MET cc_start: 0.8018 (mtp) cc_final: 0.7704 (mtm) REVERT: B 108 TYR cc_start: 0.8112 (m-10) cc_final: 0.7642 (m-80) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.1492 time to fit residues: 21.0339 Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.172557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134969 restraints weight = 5734.180| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.05 r_work: 0.3453 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5159 Z= 0.124 Angle : 0.497 5.562 6987 Z= 0.268 Chirality : 0.040 0.144 781 Planarity : 0.004 0.051 858 Dihedral : 3.822 20.552 699 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.20 % Allowed : 12.66 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 633 helix: 1.97 (0.28), residues: 333 sheet: 0.20 (0.84), residues: 46 loop : -0.34 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.025 0.001 PHE A 386 TYR 0.024 0.001 TYR A 590 ARG 0.003 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 295) hydrogen bonds : angle 4.34308 ( 879) SS BOND : bond 0.00322 ( 7) SS BOND : angle 1.12463 ( 14) covalent geometry : bond 0.00286 ( 5152) covalent geometry : angle 0.49476 ( 6973) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.7246 (t0) cc_final: 0.7017 (t0) REVERT: A 46 ILE cc_start: 0.8571 (tp) cc_final: 0.8340 (tp) REVERT: A 47 ILE cc_start: 0.8717 (mm) cc_final: 0.8449 (mm) REVERT: A 60 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8019 (mm-30) REVERT: A 70 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: A 90 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8107 (mmtm) REVERT: A 348 GLN cc_start: 0.7751 (tp40) cc_final: 0.7335 (tt0) REVERT: A 421 PHE cc_start: 0.8234 (m-80) cc_final: 0.7892 (m-80) REVERT: A 477 ASN cc_start: 0.7481 (m110) cc_final: 0.7190 (m110) REVERT: A 557 MET cc_start: 0.8085 (mmp) cc_final: 0.7627 (mmt) REVERT: A 567 LEU cc_start: 0.8630 (mp) cc_final: 0.8408 (mp) REVERT: A 649 LYS cc_start: 0.7837 (tptm) cc_final: 0.7439 (tttm) REVERT: B 58 TRP cc_start: 0.7063 (m100) cc_final: 0.6061 (m-10) REVERT: B 87 MET cc_start: 0.8047 (mtp) cc_final: 0.7689 (mtm) REVERT: B 91 LYS cc_start: 0.8089 (mttm) cc_final: 0.7880 (mttm) REVERT: B 108 TYR cc_start: 0.8160 (m-80) cc_final: 0.7611 (m-80) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.1416 time to fit residues: 21.8906 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134978 restraints weight = 5719.149| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.04 r_work: 0.3451 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5159 Z= 0.121 Angle : 0.504 9.494 6987 Z= 0.268 Chirality : 0.039 0.135 781 Planarity : 0.004 0.048 858 Dihedral : 3.769 21.289 699 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.39 % Allowed : 13.76 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.33), residues: 633 helix: 2.15 (0.28), residues: 333 sheet: 0.17 (0.84), residues: 46 loop : -0.40 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.012 0.001 PHE A 117 TYR 0.024 0.001 TYR A 590 ARG 0.002 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 295) hydrogen bonds : angle 4.24863 ( 879) SS BOND : bond 0.00322 ( 7) SS BOND : angle 1.80687 ( 14) covalent geometry : bond 0.00280 ( 5152) covalent geometry : angle 0.49844 ( 6973) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.7227 (t0) cc_final: 0.6998 (t0) REVERT: A 46 ILE cc_start: 0.8637 (tp) cc_final: 0.8426 (tp) REVERT: A 47 ILE cc_start: 0.8692 (mm) cc_final: 0.8418 (mm) REVERT: A 60 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7996 (mm-30) REVERT: A 70 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: A 90 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8073 (mmtm) REVERT: A 348 GLN cc_start: 0.7715 (tp40) cc_final: 0.7305 (tt0) REVERT: A 432 ASN cc_start: 0.7995 (m-40) cc_final: 0.7631 (m-40) REVERT: A 477 ASN cc_start: 0.7506 (m110) cc_final: 0.7249 (m110) REVERT: A 567 LEU cc_start: 0.8682 (mp) cc_final: 0.8452 (mt) REVERT: A 649 LYS cc_start: 0.7868 (tptm) cc_final: 0.7467 (tttm) REVERT: B 58 TRP cc_start: 0.7157 (m100) cc_final: 0.6159 (m-10) REVERT: B 108 TYR cc_start: 0.8219 (m-80) cc_final: 0.7675 (m-80) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.1457 time to fit residues: 21.8711 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.171099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133828 restraints weight = 5728.787| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.05 r_work: 0.3447 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5159 Z= 0.128 Angle : 0.493 5.596 6987 Z= 0.262 Chirality : 0.039 0.136 781 Planarity : 0.004 0.046 858 Dihedral : 3.762 21.260 699 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.75 % Allowed : 15.23 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.33), residues: 633 helix: 2.15 (0.28), residues: 333 sheet: 0.09 (0.83), residues: 46 loop : -0.41 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.026 0.001 PHE A 386 TYR 0.024 0.001 TYR A 590 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 295) hydrogen bonds : angle 4.24546 ( 879) SS BOND : bond 0.00231 ( 7) SS BOND : angle 1.32798 ( 14) covalent geometry : bond 0.00303 ( 5152) covalent geometry : angle 0.48990 ( 6973) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.549 Fit side-chains REVERT: A 25 ASN cc_start: 0.7276 (t0) cc_final: 0.7048 (t0) REVERT: A 46 ILE cc_start: 0.8674 (tp) cc_final: 0.8468 (tp) REVERT: A 47 ILE cc_start: 0.8704 (mm) cc_final: 0.8420 (mm) REVERT: A 60 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7993 (mm-30) REVERT: A 70 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 348 GLN cc_start: 0.7688 (tp40) cc_final: 0.7282 (tt0) REVERT: A 432 ASN cc_start: 0.8028 (m-40) cc_final: 0.7680 (m-40) REVERT: A 477 ASN cc_start: 0.7541 (m110) cc_final: 0.7272 (m110) REVERT: A 557 MET cc_start: 0.8055 (mmp) cc_final: 0.7608 (mmt) REVERT: A 605 ASN cc_start: 0.6489 (t0) cc_final: 0.5866 (p0) REVERT: A 649 LYS cc_start: 0.7868 (tptm) cc_final: 0.7462 (tttm) REVERT: B 58 TRP cc_start: 0.7165 (m100) cc_final: 0.6125 (m-10) REVERT: B 91 LYS cc_start: 0.8036 (mttm) cc_final: 0.7665 (mttp) REVERT: B 108 TYR cc_start: 0.8273 (m-80) cc_final: 0.7757 (m-80) outliers start: 15 outliers final: 12 residues processed: 107 average time/residue: 0.1352 time to fit residues: 19.8664 Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130599 restraints weight = 5677.692| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.04 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5159 Z= 0.171 Angle : 0.549 10.603 6987 Z= 0.285 Chirality : 0.041 0.142 781 Planarity : 0.004 0.044 858 Dihedral : 3.876 21.037 699 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.12 % Allowed : 15.96 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.33), residues: 633 helix: 1.98 (0.28), residues: 333 sheet: -0.11 (0.80), residues: 46 loop : -0.48 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.004 0.001 HIS B 61 PHE 0.026 0.002 PHE A 386 TYR 0.024 0.002 TYR A 590 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 295) hydrogen bonds : angle 4.38704 ( 879) SS BOND : bond 0.00291 ( 7) SS BOND : angle 1.22263 ( 14) covalent geometry : bond 0.00417 ( 5152) covalent geometry : angle 0.54705 ( 6973) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.7544 (t0) cc_final: 0.7324 (t0) REVERT: A 46 ILE cc_start: 0.8695 (tp) cc_final: 0.8493 (tp) REVERT: A 47 ILE cc_start: 0.8733 (mm) cc_final: 0.8424 (mm) REVERT: A 60 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7998 (mm-30) REVERT: A 70 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: A 348 GLN cc_start: 0.7866 (tp40) cc_final: 0.7442 (tt0) REVERT: A 432 ASN cc_start: 0.8070 (m-40) cc_final: 0.7685 (m-40) REVERT: A 477 ASN cc_start: 0.7632 (m110) cc_final: 0.7401 (m110) REVERT: A 557 MET cc_start: 0.8113 (mmp) cc_final: 0.7877 (mmp) REVERT: A 605 ASN cc_start: 0.6576 (t0) cc_final: 0.5905 (p0) REVERT: A 645 TYR cc_start: 0.7893 (t80) cc_final: 0.7489 (t80) REVERT: A 649 LYS cc_start: 0.7867 (tptm) cc_final: 0.7506 (tttm) REVERT: B 58 TRP cc_start: 0.7298 (m100) cc_final: 0.6237 (m-10) REVERT: B 108 TYR cc_start: 0.8419 (m-80) cc_final: 0.7835 (m-80) outliers start: 17 outliers final: 15 residues processed: 113 average time/residue: 0.1464 time to fit residues: 22.2020 Evaluate side-chains 117 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.169887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133186 restraints weight = 5669.740| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.00 r_work: 0.3430 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5159 Z= 0.132 Angle : 0.517 8.789 6987 Z= 0.269 Chirality : 0.040 0.138 781 Planarity : 0.004 0.044 858 Dihedral : 3.776 21.330 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 16.33 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.33), residues: 633 helix: 2.08 (0.28), residues: 333 sheet: -0.07 (0.81), residues: 46 loop : -0.50 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.027 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 295) hydrogen bonds : angle 4.29813 ( 879) SS BOND : bond 0.00290 ( 7) SS BOND : angle 1.21102 ( 14) covalent geometry : bond 0.00315 ( 5152) covalent geometry : angle 0.51438 ( 6973) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.581 Fit side-chains REVERT: A 25 ASN cc_start: 0.7483 (t0) cc_final: 0.7249 (t0) REVERT: A 47 ILE cc_start: 0.8708 (mm) cc_final: 0.8398 (mm) REVERT: A 60 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7983 (mm-30) REVERT: A 70 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 348 GLN cc_start: 0.7771 (tp40) cc_final: 0.7352 (tt0) REVERT: A 421 PHE cc_start: 0.8292 (m-80) cc_final: 0.7981 (m-80) REVERT: A 432 ASN cc_start: 0.7934 (m-40) cc_final: 0.7630 (m-40) REVERT: A 477 ASN cc_start: 0.7629 (m110) cc_final: 0.7399 (m110) REVERT: A 557 MET cc_start: 0.8073 (mmp) cc_final: 0.7826 (mmp) REVERT: A 649 LYS cc_start: 0.7867 (tptm) cc_final: 0.7500 (tttm) REVERT: B 58 TRP cc_start: 0.7291 (m100) cc_final: 0.6245 (m-10) REVERT: B 91 LYS cc_start: 0.8079 (mttm) cc_final: 0.7724 (mttp) REVERT: B 108 TYR cc_start: 0.8384 (m-80) cc_final: 0.7751 (m-80) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.1502 time to fit residues: 22.4069 Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.7282 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.169848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132992 restraints weight = 5689.518| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.01 r_work: 0.3430 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5159 Z= 0.132 Angle : 0.517 8.779 6987 Z= 0.268 Chirality : 0.040 0.137 781 Planarity : 0.004 0.044 858 Dihedral : 3.739 21.163 699 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.30 % Allowed : 16.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 633 helix: 2.11 (0.28), residues: 333 sheet: -0.05 (0.82), residues: 46 loop : -0.52 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 51 HIS 0.004 0.001 HIS B 39 PHE 0.027 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 295) hydrogen bonds : angle 4.26464 ( 879) SS BOND : bond 0.00222 ( 7) SS BOND : angle 1.12236 ( 14) covalent geometry : bond 0.00315 ( 5152) covalent geometry : angle 0.51476 ( 6973) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.518 Fit side-chains REVERT: A 25 ASN cc_start: 0.7423 (t0) cc_final: 0.7183 (t0) REVERT: A 47 ILE cc_start: 0.8689 (mm) cc_final: 0.8381 (mm) REVERT: A 60 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7981 (mm-30) REVERT: A 70 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 348 GLN cc_start: 0.7759 (tp40) cc_final: 0.7346 (tt0) REVERT: A 432 ASN cc_start: 0.7925 (m-40) cc_final: 0.7638 (m-40) REVERT: A 477 ASN cc_start: 0.7687 (m110) cc_final: 0.7418 (m110) REVERT: A 557 MET cc_start: 0.8069 (mmp) cc_final: 0.7822 (mmp) REVERT: A 567 LEU cc_start: 0.8772 (mp) cc_final: 0.8513 (mt) REVERT: A 649 LYS cc_start: 0.7906 (tptm) cc_final: 0.7499 (tttm) REVERT: B 58 TRP cc_start: 0.7246 (m100) cc_final: 0.6228 (m-10) REVERT: B 91 LYS cc_start: 0.8099 (mttm) cc_final: 0.7771 (mtmm) REVERT: B 108 TYR cc_start: 0.8398 (m-80) cc_final: 0.7781 (m-80) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.1437 time to fit residues: 21.1044 Evaluate side-chains 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.170691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133583 restraints weight = 5670.212| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.04 r_work: 0.3435 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5159 Z= 0.125 Angle : 0.510 8.470 6987 Z= 0.266 Chirality : 0.040 0.136 781 Planarity : 0.004 0.044 858 Dihedral : 3.759 21.439 699 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.12 % Allowed : 16.88 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.33), residues: 633 helix: 2.14 (0.28), residues: 333 sheet: -0.07 (0.82), residues: 46 loop : -0.51 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.026 0.001 PHE A 386 TYR 0.026 0.001 TYR A 86 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 295) hydrogen bonds : angle 4.26087 ( 879) SS BOND : bond 0.00206 ( 7) SS BOND : angle 1.05199 ( 14) covalent geometry : bond 0.00297 ( 5152) covalent geometry : angle 0.50809 ( 6973) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.574 Fit side-chains REVERT: A 25 ASN cc_start: 0.7357 (t0) cc_final: 0.7130 (t0) REVERT: A 47 ILE cc_start: 0.8681 (mm) cc_final: 0.8368 (mm) REVERT: A 60 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7998 (mm-30) REVERT: A 70 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 348 GLN cc_start: 0.7742 (tp40) cc_final: 0.7330 (tt0) REVERT: A 421 PHE cc_start: 0.8299 (m-80) cc_final: 0.8018 (m-80) REVERT: A 432 ASN cc_start: 0.7869 (m-40) cc_final: 0.7616 (m-40) REVERT: A 477 ASN cc_start: 0.7652 (m110) cc_final: 0.7405 (m110) REVERT: A 557 MET cc_start: 0.8073 (mmp) cc_final: 0.7838 (mmp) REVERT: A 567 LEU cc_start: 0.8773 (mp) cc_final: 0.8517 (mt) REVERT: A 649 LYS cc_start: 0.7925 (tptm) cc_final: 0.7532 (tttm) REVERT: B 58 TRP cc_start: 0.7218 (m100) cc_final: 0.6190 (m-10) REVERT: B 91 LYS cc_start: 0.8143 (mttm) cc_final: 0.7905 (mtmm) REVERT: B 108 TYR cc_start: 0.8400 (m-80) cc_final: 0.7792 (m-80) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.1370 time to fit residues: 19.5555 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.0020 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.163659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129656 restraints weight = 5873.887| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.87 r_work: 0.3241 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5159 Z= 0.111 Angle : 0.492 8.334 6987 Z= 0.255 Chirality : 0.039 0.134 781 Planarity : 0.004 0.044 858 Dihedral : 3.650 20.987 699 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.75 % Allowed : 17.06 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.34), residues: 633 helix: 2.23 (0.28), residues: 333 sheet: 0.00 (0.81), residues: 46 loop : -0.42 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 51 HIS 0.003 0.001 HIS B 61 PHE 0.027 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 295) hydrogen bonds : angle 4.17965 ( 879) SS BOND : bond 0.00190 ( 7) SS BOND : angle 0.98482 ( 14) covalent geometry : bond 0.00258 ( 5152) covalent geometry : angle 0.49013 ( 6973) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.07 seconds wall clock time: 53 minutes 34.91 seconds (3214.91 seconds total)