Starting phenix.real_space_refine on Wed Jan 22 19:31:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.map" model { file = "/net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chp_45597/01_2025/9chp_45597.cif" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 10.90, per 1000 atoms: 0.57 Number of scatterers: 19104 At special positions: 0 Unit cell: (122.85, 122.85, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS A 525 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 575 Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 687 Processing helix chain 'A' and resid 690 through 709 Processing helix chain 'B' and resid 404 through 432 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL B 535 " --> pdb=" O ARG B 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 575 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 687 Processing helix chain 'B' and resid 690 through 709 Processing helix chain 'C' and resid 404 through 432 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 512 Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 575 Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 687 Processing helix chain 'C' and resid 690 through 709 Processing helix chain 'D' and resid 404 through 432 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 472 removed outlier: 3.692A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 496 removed outlier: 3.635A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 507 through 512 Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.726A pdb=" N LYS D 525 " --> pdb=" O ILE D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 Processing helix chain 'D' and resid 531 through 538 removed outlier: 3.928A pdb=" N VAL D 535 " --> pdb=" O ARG D 531 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 575 Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.571A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.709A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 687 Processing helix chain 'D' and resid 690 through 709 680 hydrogen bonds defined for protein. 2016 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: 7.71 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1520 1.30 - 1.48: 4040 1.48 - 1.65: 4152 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" CE2 PHE B 686 " pdb=" HE2 PHE B 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE D 686 " pdb=" HE2 PHE D 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE C 686 " pdb=" HE2 PHE C 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE A 686 " pdb=" HE2 PHE A 686 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN A 691 " pdb=" H ASN A 691 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 29473 2.54 - 5.08: 4211 5.08 - 7.62: 1164 7.62 - 10.16: 48 10.16 - 12.70: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CB HIS A 587 " pdb=" CG HIS A 587 " pdb=" CD2 HIS A 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS D 587 " pdb=" CG HIS D 587 " pdb=" CD2 HIS D 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS C 587 " pdb=" CG HIS C 587 " pdb=" CD2 HIS C 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CB HIS B 587 " pdb=" CG HIS B 587 " pdb=" CD2 HIS B 587 " ideal model delta sigma weight residual 131.20 124.72 6.48 1.30e+00 5.92e-01 2.49e+01 angle pdb=" CA ASP A 540 " pdb=" CB ASP A 540 " pdb=" CG ASP A 540 " ideal model delta sigma weight residual 112.60 117.30 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 8412 15.62 - 31.24: 456 31.24 - 46.86: 152 46.86 - 62.48: 92 62.48 - 78.10: 12 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" CA HIS B 578 " pdb=" C HIS B 578 " pdb=" N MET B 579 " pdb=" CA MET B 579 " ideal model delta harmonic sigma weight residual 180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA HIS C 578 " pdb=" C HIS C 578 " pdb=" N MET C 579 " pdb=" CA MET C 579 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA HIS D 578 " pdb=" C HIS D 578 " pdb=" N MET D 579 " pdb=" CA MET D 579 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 948 0.081 - 0.163: 448 0.163 - 0.244: 76 0.244 - 0.326: 20 0.326 - 0.407: 4 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER A 624 " pdb=" N SER A 624 " pdb=" C SER A 624 " pdb=" CB SER A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA SER D 624 " pdb=" N SER D 624 " pdb=" C SER D 624 " pdb=" CB SER D 624 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG A 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG A 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG A 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG A 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG A 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG A 534 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG D 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG D 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG D 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG D 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG D 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG D 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG D 534 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 534 " 0.508 9.50e-02 1.11e+02 1.85e-01 1.52e+02 pdb=" NE ARG C 534 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 534 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG C 534 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG C 534 " -0.035 2.00e-02 2.50e+03 pdb="HH11 ARG C 534 " -0.171 2.00e-02 2.50e+03 pdb="HH12 ARG C 534 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG C 534 " -0.029 2.00e-02 2.50e+03 pdb="HH22 ARG C 534 " -0.026 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1016 2.21 - 2.81: 34968 2.81 - 3.41: 52855 3.41 - 4.00: 68966 4.00 - 4.60: 99356 Nonbonded interactions: 257161 Sorted by model distance: nonbonded pdb=" OE2 GLU A 575 " pdb=" HG SER A 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU B 575 " pdb=" HG SER B 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.614 2.450 nonbonded pdb=" HH TYR B 420 " pdb=" OD1 ASP B 456 " model vdw 1.625 2.450 ... (remaining 257156 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.470 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: 0.350 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.930 Find NCS groups from input model: 0.470 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 0.013 0.042 9776 Z= 0.825 Angle : 1.747 8.061 13288 Z= 1.208 Chirality : 0.092 0.407 1496 Planarity : 0.018 0.163 1620 Dihedral : 11.611 78.104 3420 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.91 (0.24), residues: 1140 helix: -0.82 (0.15), residues: 904 sheet: None (None), residues: 0 loop : 1.22 (0.52), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.019 TRP B 705 HIS 0.010 0.003 HIS B 587 PHE 0.069 0.014 PHE C 701 TYR 0.136 0.023 TYR B 652 ARG 0.008 0.001 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7094 (tpt) cc_final: 0.6808 (tpt) REVERT: A 688 GLN cc_start: 0.8171 (mt0) cc_final: 0.7498 (tm-30) REVERT: B 502 MET cc_start: 0.7023 (tpt) cc_final: 0.6745 (tpt) REVERT: B 688 GLN cc_start: 0.8118 (mt0) cc_final: 0.7488 (tm-30) REVERT: C 502 MET cc_start: 0.7079 (tpt) cc_final: 0.6797 (tpt) REVERT: C 688 GLN cc_start: 0.8181 (mt0) cc_final: 0.7479 (tm-30) REVERT: D 502 MET cc_start: 0.7103 (tpt) cc_final: 0.6819 (tpt) REVERT: D 688 GLN cc_start: 0.8177 (mt0) cc_final: 0.7494 (tm-30) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.5670 time to fit residues: 144.0514 Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 687 HIS B 674 HIS B 687 HIS C 674 HIS C 687 HIS D 674 HIS D 687 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.174324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116821 restraints weight = 28904.681| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.40 r_work: 0.2991 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9776 Z= 0.219 Angle : 0.584 7.216 13288 Z= 0.322 Chirality : 0.040 0.127 1496 Planarity : 0.005 0.058 1620 Dihedral : 4.835 24.507 1280 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 2.84 % Favored : 96.37 % 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: 1.12 (0.25), residues: 1140 helix: 0.66 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.70 (0.51), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 585 HIS 0.003 0.001 HIS A 687 PHE 0.014 0.002 PHE A 656 TYR 0.015 0.002 TYR A 611 ARG 0.003 0.001 ARG D 665 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLU cc_start: 0.5570 (mt-10) cc_final: 0.5261 (tp30) REVERT: A 502 MET cc_start: 0.6907 (tpt) cc_final: 0.6534 (tpt) REVERT: B 481 GLU cc_start: 0.5567 (mt-10) cc_final: 0.5266 (tp30) REVERT: B 502 MET cc_start: 0.6907 (tpt) cc_final: 0.6536 (tpt) REVERT: C 481 GLU cc_start: 0.5546 (mt-10) cc_final: 0.5262 (tp30) REVERT: C 502 MET cc_start: 0.6909 (tpt) cc_final: 0.6528 (tpt) REVERT: D 481 GLU cc_start: 0.5560 (mt-10) cc_final: 0.5264 (tp30) REVERT: D 502 MET cc_start: 0.6894 (tpt) cc_final: 0.6520 (tpt) outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.6240 time to fit residues: 129.4411 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.171122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115445 restraints weight = 28881.224| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.22 r_work: 0.2943 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9776 Z= 0.283 Angle : 0.558 7.969 13288 Z= 0.308 Chirality : 0.040 0.132 1496 Planarity : 0.004 0.048 1620 Dihedral : 4.481 23.192 1280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.39 % Allowed : 6.37 % Favored : 93.24 % 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 (0.25), residues: 1140 helix: 0.95 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.38 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 585 HIS 0.003 0.001 HIS A 402 PHE 0.012 0.002 PHE C 656 TYR 0.014 0.002 TYR A 616 ARG 0.003 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7019 (tpt) cc_final: 0.6582 (tpt) REVERT: B 502 MET cc_start: 0.7010 (tpt) cc_final: 0.6572 (tpt) REVERT: C 502 MET cc_start: 0.7011 (tpt) cc_final: 0.6575 (tpt) REVERT: D 502 MET cc_start: 0.7011 (tpt) cc_final: 0.6577 (tpt) outliers start: 4 outliers final: 4 residues processed: 152 average time/residue: 0.5627 time to fit residues: 114.4809 Evaluate side-chains 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.186360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130616 restraints weight = 28223.650| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.97 r_work: 0.3036 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9776 Z= 0.192 Angle : 0.480 6.456 13288 Z= 0.260 Chirality : 0.037 0.135 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.205 22.544 1280 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.78 % Allowed : 6.76 % Favored : 92.45 % 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: 1.90 (0.25), residues: 1140 helix: 1.24 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.84 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 585 HIS 0.002 0.001 HIS A 674 PHE 0.010 0.001 PHE D 656 TYR 0.013 0.001 TYR A 616 ARG 0.005 0.000 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7206 (tpt) cc_final: 0.6759 (tpt) REVERT: B 502 MET cc_start: 0.7188 (tpt) cc_final: 0.6735 (tpt) REVERT: C 502 MET cc_start: 0.7170 (tpt) cc_final: 0.6715 (tpt) REVERT: D 502 MET cc_start: 0.7214 (tpt) cc_final: 0.6758 (tpt) outliers start: 8 outliers final: 8 residues processed: 154 average time/residue: 0.6036 time to fit residues: 122.4351 Evaluate side-chains 150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.174040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116004 restraints weight = 28793.496| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.03 r_work: 0.3056 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9776 Z= 0.155 Angle : 0.436 4.576 13288 Z= 0.238 Chirality : 0.037 0.135 1496 Planarity : 0.004 0.041 1620 Dihedral : 3.928 20.571 1280 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.27 % Allowed : 7.35 % Favored : 91.37 % 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: 2.29 (0.25), residues: 1140 helix: 1.53 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.90 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.000 HIS C 674 PHE 0.009 0.001 PHE B 656 TYR 0.012 0.001 TYR D 616 ARG 0.001 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: B 462 MET cc_start: 0.7700 (ttm) cc_final: 0.7472 (mtm) REVERT: B 652 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: C 462 MET cc_start: 0.7705 (ttm) cc_final: 0.7478 (mtm) REVERT: C 652 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6400 (m-80) REVERT: D 462 MET cc_start: 0.7715 (ttm) cc_final: 0.7487 (mtm) REVERT: D 652 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6413 (m-80) outliers start: 13 outliers final: 4 residues processed: 157 average time/residue: 0.5591 time to fit residues: 118.0782 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 652 TYR Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 652 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN B 576 GLN C 576 GLN D 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.173681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121079 restraints weight = 28895.980| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.25 r_work: 0.3048 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.181 Angle : 0.449 4.536 13288 Z= 0.244 Chirality : 0.037 0.136 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.867 20.338 1280 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.27 % Allowed : 7.35 % Favored : 91.37 % 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: 2.44 (0.25), residues: 1140 helix: 1.55 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 2.37 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 568 HIS 0.002 0.001 HIS A 674 PHE 0.011 0.001 PHE C 656 TYR 0.013 0.001 TYR A 616 ARG 0.002 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 156 average time/residue: 0.5589 time to fit residues: 117.5542 Evaluate side-chains 164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.173417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119990 restraints weight = 28653.431| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.188 Angle : 0.445 4.544 13288 Z= 0.241 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.821 20.043 1280 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.47 % Allowed : 7.25 % Favored : 91.27 % 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: 2.52 (0.25), residues: 1140 helix: 1.62 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 2.34 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 585 HIS 0.002 0.001 HIS A 402 PHE 0.010 0.001 PHE A 656 TYR 0.014 0.001 TYR D 616 ARG 0.002 0.000 ARG D 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 MET cc_start: 0.7817 (ttm) cc_final: 0.7554 (ttm) REVERT: C 462 MET cc_start: 0.7793 (ttm) cc_final: 0.7526 (ttm) REVERT: D 462 MET cc_start: 0.7814 (ttm) cc_final: 0.7551 (ttm) outliers start: 15 outliers final: 12 residues processed: 156 average time/residue: 0.5514 time to fit residues: 116.8436 Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 709 ASN C 709 ASN D 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115689 restraints weight = 29092.587| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.13 r_work: 0.2980 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9776 Z= 0.254 Angle : 0.488 4.600 13288 Z= 0.266 Chirality : 0.038 0.136 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.937 20.159 1280 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.18 % Allowed : 8.73 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.25), residues: 1140 helix: 1.50 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.99 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.002 0.001 HIS C 703 PHE 0.012 0.001 PHE D 656 TYR 0.015 0.002 TYR D 616 ARG 0.003 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 144 average time/residue: 0.5943 time to fit residues: 114.5072 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.188663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130927 restraints weight = 28310.605| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.16 r_work: 0.2968 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.169 Angle : 0.441 4.594 13288 Z= 0.236 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.795 19.978 1280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 9.12 % Favored : 89.71 % 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: 2.52 (0.25), residues: 1140 helix: 1.67 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 2.07 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.001 0.001 HIS D 674 PHE 0.010 0.001 PHE A 656 TYR 0.013 0.001 TYR B 616 ARG 0.002 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 MET cc_start: 0.7531 (ttm) cc_final: 0.7271 (ttm) REVERT: C 462 MET cc_start: 0.7520 (ttm) cc_final: 0.7256 (ttm) REVERT: D 462 MET cc_start: 0.7535 (ttm) cc_final: 0.7274 (ttm) outliers start: 12 outliers final: 12 residues processed: 148 average time/residue: 0.5684 time to fit residues: 112.2291 Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 635 ASN C 635 ASN D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.188585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129863 restraints weight = 28449.852| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.08 r_work: 0.2983 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.179 Angle : 0.446 4.582 13288 Z= 0.239 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.754 19.676 1280 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.18 % Allowed : 9.51 % Favored : 89.31 % 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: 2.53 (0.25), residues: 1140 helix: 1.70 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.98 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 568 HIS 0.001 0.001 HIS C 402 PHE 0.010 0.001 PHE A 656 TYR 0.014 0.001 TYR C 616 ARG 0.002 0.000 ARG A 537 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.558 Fit side-chains REVERT: B 462 MET cc_start: 0.7575 (ttm) cc_final: 0.7305 (ttm) REVERT: C 462 MET cc_start: 0.7562 (ttm) cc_final: 0.7287 (ttm) REVERT: D 462 MET cc_start: 0.7575 (ttm) cc_final: 0.7304 (ttm) outliers start: 12 outliers final: 12 residues processed: 151 average time/residue: 0.5620 time to fit residues: 114.1601 Evaluate side-chains 159 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 635 ASN C 635 ASN D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.188000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134452 restraints weight = 28110.206| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.09 r_work: 0.3068 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9776 Z= 0.176 Angle : 0.448 4.598 13288 Z= 0.240 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.047 1620 Dihedral : 3.744 19.531 1280 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 9.51 % Favored : 89.31 % 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: 2.55 (0.25), residues: 1140 helix: 1.72 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.97 (0.48), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.002 0.001 HIS D 674 PHE 0.010 0.001 PHE A 656 TYR 0.014 0.001 TYR B 616 ARG 0.008 0.000 ARG C 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9985.83 seconds wall clock time: 176 minutes 18.66 seconds (10578.66 seconds total)