Starting phenix.real_space_refine on Thu Sep 18 18:14:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chp_45597/09_2025/9chp_45597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chp_45597/09_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_45597/09_2025/9chp_45597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chp_45597/09_2025/9chp_45597.map" model { file = "/net/cci-nas-00/data/ceres_data/9chp_45597/09_2025/9chp_45597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chp_45597/09_2025/9chp_45597.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D Time building chain proxies: 4.00, per 1000 atoms: 0.21 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: 1.36 Conformation dependent library (CDL) restraints added in 508.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.39 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: 3.93 Time building geometry restraints manager: 1.90 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 2.580 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: 0.110 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.220 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- 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= 0.773 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 531 TYR 0.136 0.023 TYR B 652 PHE 0.069 0.014 PHE C 701 TRP 0.107 0.019 TRP B 705 HIS 0.010 0.003 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.01300 ( 9776) covalent geometry : angle 1.74666 (13288) hydrogen bonds : bond 0.16597 ( 680) hydrogen bonds : angle 6.67709 ( 2016) *********************** 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 : 0.374 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: 0.6803 (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: 0.6741 (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: 0.6793 (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: 0.6814 (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: 0.2425 time to fit residues: 61.6453 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 : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.174845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132867 restraints weight = 29112.917| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.43 r_work: 0.3084 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2594 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= 0.146 Angle : 0.576 7.189 13288 Z= 0.318 Chirality : 0.040 0.130 1496 Planarity : 0.005 0.057 1620 Dihedral : 4.800 24.426 1280 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.25), residues: 1140 helix: 0.68 (0.16), residues: 912 sheet: None (None), residues: 0 loop : 1.84 (0.52), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 582 TYR 0.015 0.002 TYR A 611 PHE 0.013 0.002 PHE D 656 TRP 0.012 0.001 TRP D 585 HIS 0.003 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9776) covalent geometry : angle 0.57622 (13288) hydrogen bonds : bond 0.05266 ( 680) hydrogen bonds : angle 4.35238 ( 2016) *********************** 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 : 0.432 Fit side-chains REVERT: A 502 MET cc_start: 0.6910 (tpt) cc_final: 0.6518 (tpt) REVERT: B 502 MET cc_start: 0.6912 (tpt) cc_final: 0.6521 (tpt) REVERT: C 502 MET cc_start: 0.6907 (tpt) cc_final: 0.6513 (tpt) REVERT: D 502 MET cc_start: 0.6898 (tpt) cc_final: 0.6504 (tpt) outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.2557 time to fit residues: 52.6528 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.172191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119673 restraints weight = 29230.090| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.61 r_work: 0.2962 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9776 Z= 0.176 Angle : 0.537 7.878 13288 Z= 0.293 Chirality : 0.039 0.133 1496 Planarity : 0.004 0.045 1620 Dihedral : 4.414 23.021 1280 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.39 % Allowed : 5.59 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.25), residues: 1140 helix: 1.06 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.62 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 541 TYR 0.013 0.002 TYR D 616 PHE 0.010 0.001 PHE B 656 TRP 0.012 0.001 TRP B 585 HIS 0.003 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9776) covalent geometry : angle 0.53685 (13288) hydrogen bonds : bond 0.04508 ( 680) hydrogen bonds : angle 4.12394 ( 2016) *********************** 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 : 0.375 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.6987 (tpt) cc_final: 0.6539 (tpt) REVERT: B 502 MET cc_start: 0.6999 (tpt) cc_final: 0.6552 (tpt) REVERT: C 502 MET cc_start: 0.6987 (tpt) cc_final: 0.6541 (tpt) REVERT: D 502 MET cc_start: 0.6990 (tpt) cc_final: 0.6547 (tpt) outliers start: 4 outliers final: 4 residues processed: 152 average time/residue: 0.2310 time to fit residues: 46.9440 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.184143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127308 restraints weight = 28505.471| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.02 r_work: 0.3089 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9776 Z= 0.132 Angle : 0.468 6.293 13288 Z= 0.253 Chirality : 0.037 0.134 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.114 22.169 1280 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.78 % Allowed : 5.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.25), residues: 1140 helix: 1.32 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.85 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 679 TYR 0.013 0.001 TYR D 616 PHE 0.010 0.001 PHE A 656 TRP 0.009 0.001 TRP D 705 HIS 0.001 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9776) covalent geometry : angle 0.46787 (13288) hydrogen bonds : bond 0.03973 ( 680) hydrogen bonds : angle 3.92646 ( 2016) *********************** 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 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7150 (tpt) cc_final: 0.6709 (tpt) REVERT: B 502 MET cc_start: 0.7121 (tpt) cc_final: 0.6673 (tpt) REVERT: C 502 MET cc_start: 0.7112 (tpt) cc_final: 0.6662 (tpt) REVERT: D 502 MET cc_start: 0.7164 (tpt) cc_final: 0.6713 (tpt) outliers start: 8 outliers final: 8 residues processed: 158 average time/residue: 0.2268 time to fit residues: 48.3307 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 : 0.417 ------------------------------------------------------------------------------- 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 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.183698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123337 restraints weight = 28682.982| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.15 r_work: 0.2975 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3603 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= 0.129 Angle : 0.451 4.573 13288 Z= 0.247 Chirality : 0.037 0.135 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.968 20.778 1280 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.27 % Allowed : 6.67 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.25), residues: 1140 helix: 1.42 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.91 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 679 TYR 0.013 0.001 TYR B 616 PHE 0.010 0.001 PHE D 656 TRP 0.009 0.001 TRP C 568 HIS 0.002 0.001 HIS D 674 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9776) covalent geometry : angle 0.45115 (13288) hydrogen bonds : bond 0.03899 ( 680) hydrogen bonds : angle 3.82700 ( 2016) *********************** 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 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7078 (tpt) cc_final: 0.6612 (tpt) REVERT: B 462 MET cc_start: 0.7546 (ttm) cc_final: 0.7267 (ttm) REVERT: B 502 MET cc_start: 0.7061 (tpt) cc_final: 0.6589 (tpt) REVERT: C 462 MET cc_start: 0.7538 (ttm) cc_final: 0.7258 (ttm) REVERT: C 502 MET cc_start: 0.7060 (tpt) cc_final: 0.6590 (tpt) REVERT: D 462 MET cc_start: 0.7552 (ttm) cc_final: 0.7284 (ttm) REVERT: D 502 MET cc_start: 0.7079 (tpt) cc_final: 0.6595 (tpt) outliers start: 13 outliers final: 12 residues processed: 160 average time/residue: 0.2454 time to fit residues: 51.7455 Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 470 ASN Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 682 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.176468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122308 restraints weight = 28504.009| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.28 r_work: 0.3149 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9776 Z= 0.102 Angle : 0.427 4.494 13288 Z= 0.230 Chirality : 0.036 0.137 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.819 20.216 1280 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.86 % Allowed : 6.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.25), residues: 1140 helix: 1.57 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 2.20 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 528 TYR 0.012 0.001 TYR A 616 PHE 0.009 0.001 PHE A 656 TRP 0.008 0.001 TRP B 568 HIS 0.001 0.000 HIS D 674 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9776) covalent geometry : angle 0.42696 (13288) hydrogen bonds : bond 0.03583 ( 680) hydrogen bonds : angle 3.66673 ( 2016) *********************** 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 163 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 502 MET cc_start: 0.7204 (tpt) cc_final: 0.6694 (tpt) REVERT: C 502 MET cc_start: 0.7212 (tpt) cc_final: 0.6700 (tpt) REVERT: D 502 MET cc_start: 0.7227 (tpt) cc_final: 0.6711 (tpt) outliers start: 19 outliers final: 10 residues processed: 148 average time/residue: 0.2409 time to fit residues: 47.6180 Evaluate side-chains 150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 554 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.173546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133287 restraints weight = 28790.544| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.50 r_work: 0.3297 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9776 Z= 0.151 Angle : 0.468 4.574 13288 Z= 0.257 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.889 19.970 1280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.27 % Allowed : 7.06 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.25), residues: 1140 helix: 1.53 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 2.32 (0.49), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 679 TYR 0.015 0.001 TYR D 616 PHE 0.012 0.001 PHE D 656 TRP 0.009 0.001 TRP D 585 HIS 0.002 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9776) covalent geometry : angle 0.46801 (13288) hydrogen bonds : bond 0.03893 ( 680) hydrogen bonds : angle 3.74817 ( 2016) *********************** 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 165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7370 (tpt) cc_final: 0.7068 (tpt) REVERT: B 502 MET cc_start: 0.7313 (tpt) cc_final: 0.6827 (tpt) REVERT: C 502 MET cc_start: 0.7308 (tpt) cc_final: 0.6818 (tpt) REVERT: D 502 MET cc_start: 0.7321 (tpt) cc_final: 0.6834 (tpt) outliers start: 13 outliers final: 12 residues processed: 153 average time/residue: 0.2289 time to fit residues: 46.2296 Evaluate side-chains 158 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.181339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124543 restraints weight = 28710.866| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.98 r_work: 0.3020 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9776 Z= 0.211 Angle : 0.515 4.601 13288 Z= 0.287 Chirality : 0.040 0.134 1496 Planarity : 0.004 0.041 1620 Dihedral : 4.107 20.364 1280 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.88 % Allowed : 8.53 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.25), residues: 1140 helix: 1.19 (0.16), residues: 912 sheet: None (None), residues: 0 loop : 1.85 (0.49), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 528 TYR 0.015 0.002 TYR D 616 PHE 0.014 0.002 PHE C 656 TRP 0.011 0.002 TRP C 585 HIS 0.002 0.001 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9776) covalent geometry : angle 0.51493 (13288) hydrogen bonds : bond 0.04385 ( 680) hydrogen bonds : angle 3.92651 ( 2016) *********************** 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 161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.7389 (tpt) cc_final: 0.7074 (tpt) REVERT: A 538 LYS cc_start: 0.7904 (mttt) cc_final: 0.7627 (mttt) REVERT: A 679 ARG cc_start: 0.6463 (mtp180) cc_final: 0.6158 (mtm110) REVERT: B 502 MET cc_start: 0.7362 (tpt) cc_final: 0.6864 (tpt) REVERT: B 538 LYS cc_start: 0.7907 (mttt) cc_final: 0.7615 (mttt) REVERT: B 679 ARG cc_start: 0.6429 (mtp180) cc_final: 0.6129 (mtm110) REVERT: C 502 MET cc_start: 0.7363 (tpt) cc_final: 0.6862 (tpt) REVERT: C 538 LYS cc_start: 0.7895 (mttt) cc_final: 0.7596 (mttt) REVERT: C 679 ARG cc_start: 0.6471 (mtp180) cc_final: 0.6163 (mtm110) REVERT: D 502 MET cc_start: 0.7387 (tpt) cc_final: 0.6890 (tpt) REVERT: D 538 LYS cc_start: 0.7913 (mttt) cc_final: 0.7624 (mttt) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.2285 time to fit residues: 46.3914 Evaluate side-chains 155 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.186311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130011 restraints weight = 28085.655| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.96 r_work: 0.3012 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9776 Z= 0.142 Angle : 0.457 4.603 13288 Z= 0.250 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.947 20.486 1280 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.37 % Allowed : 8.14 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1140 helix: 1.43 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.82 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.013 0.002 TYR B 616 PHE 0.011 0.001 PHE B 656 TRP 0.010 0.001 TRP B 568 HIS 0.002 0.001 HIS D 674 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9776) covalent geometry : angle 0.45655 (13288) hydrogen bonds : bond 0.03935 ( 680) hydrogen bonds : angle 3.78235 ( 2016) *********************** 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 164 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.7342 (tpt) cc_final: 0.7045 (tpt) REVERT: A 679 ARG cc_start: 0.6478 (mtp180) cc_final: 0.6199 (mtm110) REVERT: B 502 MET cc_start: 0.7352 (tpt) cc_final: 0.6860 (tpt) REVERT: B 679 ARG cc_start: 0.6478 (mtp180) cc_final: 0.6186 (mtm110) REVERT: C 502 MET cc_start: 0.7357 (tpt) cc_final: 0.6863 (tpt) REVERT: C 679 ARG cc_start: 0.6499 (mtp180) cc_final: 0.6208 (mtm110) REVERT: D 502 MET cc_start: 0.7378 (tpt) cc_final: 0.6878 (tpt) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 0.2368 time to fit residues: 47.4619 Evaluate side-chains 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.187715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131171 restraints weight = 28228.981| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.98 r_work: 0.3026 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4097 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= 0.126 Angle : 0.441 4.591 13288 Z= 0.239 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.041 1620 Dihedral : 3.811 19.908 1280 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 9.02 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.25), residues: 1140 helix: 1.59 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.95 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.014 0.001 TYR A 616 PHE 0.010 0.001 PHE D 656 TRP 0.010 0.001 TRP B 568 HIS 0.002 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9776) covalent geometry : angle 0.44131 (13288) hydrogen bonds : bond 0.03713 ( 680) hydrogen bonds : angle 3.67386 ( 2016) ********************** 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 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 502 MET cc_start: 0.7324 (tpt) cc_final: 0.6910 (tpt) REVERT: A 679 ARG cc_start: 0.6467 (mtp180) cc_final: 0.6206 (mtm110) REVERT: B 502 MET cc_start: 0.7295 (tpt) cc_final: 0.6804 (tpt) REVERT: B 679 ARG cc_start: 0.6461 (mtp180) cc_final: 0.6197 (mtm110) REVERT: C 502 MET cc_start: 0.7305 (tpt) cc_final: 0.6807 (tpt) REVERT: C 679 ARG cc_start: 0.6497 (mtp180) cc_final: 0.6229 (mtm110) REVERT: D 502 MET cc_start: 0.7319 (tpt) cc_final: 0.6827 (tpt) outliers start: 12 outliers final: 12 residues processed: 148 average time/residue: 0.2367 time to fit residues: 46.9802 Evaluate side-chains 157 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.187310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130568 restraints weight = 28270.225| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.00 r_work: 0.3016 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9776 Z= 0.133 Angle : 0.448 4.586 13288 Z= 0.243 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.796 19.654 1280 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.08 % Allowed : 9.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.25), residues: 1140 helix: 1.59 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.86 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 528 TYR 0.014 0.001 TYR A 616 PHE 0.010 0.001 PHE A 656 TRP 0.009 0.001 TRP B 568 HIS 0.002 0.001 HIS C 674 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9776) covalent geometry : angle 0.44768 (13288) hydrogen bonds : bond 0.03761 ( 680) hydrogen bonds : angle 3.67673 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.85 seconds wall clock time: 79 minutes 36.10 seconds (4776.10 seconds total)