Starting phenix.real_space_refine on Mon Jun 16 19:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chp_45597/06_2025/9chp_45597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chp_45597/06_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_45597/06_2025/9chp_45597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chp_45597/06_2025/9chp_45597.map" model { file = "/net/cci-nas-00/data/ceres_data/9chp_45597/06_2025/9chp_45597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chp_45597/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.41, per 1000 atoms: 0.54 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: 4.62 Conformation dependent library (CDL) restraints added in 1.4 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: 1.30 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: 6.25 Time building geometry restraints manager: 5.68 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: 0.07 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: 2.140 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: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.050 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16597 ( 680) hydrogen bonds : angle 6.67709 ( 2016) covalent geometry : bond 0.01300 ( 9776) covalent geometry : angle 1.74666 (13288) *********************** 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 : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.5703 time to fit residues: 145.5046 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 : 1.409 ------------------------------------------------------------------------------- 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 = 95)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120316 restraints weight = 28904.681| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.27 r_work: 0.2977 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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= 0.156 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 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 680) hydrogen bonds : angle 4.36634 ( 2016) covalent geometry : bond 0.00339 ( 9776) covalent geometry : angle 0.58360 (13288) *********************** 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 : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.6847 (tpt) cc_final: 0.6455 (tpt) REVERT: B 502 MET cc_start: 0.6849 (tpt) cc_final: 0.6457 (tpt) REVERT: C 502 MET cc_start: 0.6843 (tpt) cc_final: 0.6446 (tpt) REVERT: D 502 MET cc_start: 0.6835 (tpt) cc_final: 0.6443 (tpt) outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.6182 time to fit residues: 128.1578 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 : 1.447 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.171256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110907 restraints weight = 29027.653| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.11 r_work: 0.2949 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3181 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= 0.193 Angle : 0.562 8.250 13288 Z= 0.310 Chirality : 0.040 0.132 1496 Planarity : 0.004 0.048 1620 Dihedral : 4.464 23.138 1280 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.39 % Allowed : 5.98 % Favored : 93.63 % 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: 1.41 (0.25), residues: 1140 helix: 0.96 (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 B 585 HIS 0.003 0.001 HIS A 402 PHE 0.012 0.002 PHE A 656 TYR 0.014 0.002 TYR A 616 ARG 0.003 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 680) hydrogen bonds : angle 4.19111 ( 2016) covalent geometry : bond 0.00439 ( 9776) covalent geometry : angle 0.56189 (13288) *********************** 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 : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7032 (tpt) cc_final: 0.6592 (tpt) REVERT: B 502 MET cc_start: 0.7024 (tpt) cc_final: 0.6587 (tpt) REVERT: C 502 MET cc_start: 0.7024 (tpt) cc_final: 0.6586 (tpt) REVERT: D 502 MET cc_start: 0.7025 (tpt) cc_final: 0.6590 (tpt) outliers start: 4 outliers final: 4 residues processed: 152 average time/residue: 0.7485 time to fit residues: 161.3617 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 : 1.462 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.172705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118244 restraints weight = 28894.808| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.34 r_work: 0.2959 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3472 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= 0.134 Angle : 0.457 4.563 13288 Z= 0.252 Chirality : 0.037 0.135 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.164 22.471 1280 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.18 % Allowed : 5.98 % Favored : 92.84 % 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: 1.93 (0.25), residues: 1140 helix: 1.27 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 1.81 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 705 HIS 0.001 0.001 HIS A 492 PHE 0.010 0.001 PHE A 656 TYR 0.013 0.001 TYR D 616 ARG 0.003 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 680) hydrogen bonds : angle 3.95949 ( 2016) covalent geometry : bond 0.00294 ( 9776) covalent geometry : angle 0.45672 (13288) *********************** 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: 12 poor density : 154 time to evaluate : 1.815 Fit side-chains REVERT: A 502 MET cc_start: 0.7111 (tpt) cc_final: 0.6658 (tpt) REVERT: A 652 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: B 502 MET cc_start: 0.7090 (tpt) cc_final: 0.6637 (tpt) REVERT: B 652 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: C 502 MET cc_start: 0.7080 (tpt) cc_final: 0.6624 (tpt) REVERT: C 652 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: D 502 MET cc_start: 0.7110 (tpt) cc_final: 0.6658 (tpt) REVERT: D 652 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6417 (m-80) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.6533 time to fit residues: 139.5443 Evaluate side-chains 154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 652 TYR Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 652 TYR Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 682 GLU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 652 TYR 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.189399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133950 restraints weight = 28293.787| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.93 r_work: 0.3027 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9776 Z= 0.154 Angle : 0.480 4.637 13288 Z= 0.265 Chirality : 0.038 0.134 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.102 21.243 1280 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.88 % Allowed : 7.35 % Favored : 91.76 % 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: 1.86 (0.25), residues: 1140 helix: 1.26 (0.16), residues: 912 sheet: None (None), residues: 0 loop : 1.63 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 585 HIS 0.002 0.001 HIS C 402 PHE 0.012 0.001 PHE C 656 TYR 0.014 0.002 TYR C 616 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 680) hydrogen bonds : angle 3.89910 ( 2016) covalent geometry : bond 0.00348 ( 9776) covalent geometry : angle 0.48038 (13288) *********************** 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 161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7314 (tpt) cc_final: 0.6836 (tpt) REVERT: B 462 MET cc_start: 0.7792 (ttm) cc_final: 0.7545 (ttm) REVERT: B 502 MET cc_start: 0.7277 (tpt) cc_final: 0.6798 (tpt) REVERT: C 462 MET cc_start: 0.7791 (ttm) cc_final: 0.7537 (ttm) REVERT: C 502 MET cc_start: 0.7258 (tpt) cc_final: 0.6778 (tpt) REVERT: D 462 MET cc_start: 0.7815 (ttm) cc_final: 0.7566 (ttm) REVERT: D 502 MET cc_start: 0.7303 (tpt) cc_final: 0.6825 (tpt) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.5446 time to fit residues: 110.9049 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 : 1.368 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.182264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127194 restraints weight = 28572.556| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.10 r_work: 0.2952 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9776 Z= 0.163 Angle : 0.474 4.550 13288 Z= 0.261 Chirality : 0.038 0.134 1496 Planarity : 0.004 0.041 1620 Dihedral : 4.063 21.083 1280 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 7.84 % 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 (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: 1.98 (0.25), residues: 1140 helix: 1.27 (0.16), residues: 912 sheet: None (None), residues: 0 loop : 2.00 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 585 HIS 0.002 0.001 HIS D 402 PHE 0.012 0.001 PHE A 656 TYR 0.014 0.002 TYR C 616 ARG 0.003 0.000 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 680) hydrogen bonds : angle 3.89135 ( 2016) covalent geometry : bond 0.00371 ( 9776) covalent geometry : angle 0.47433 (13288) *********************** 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 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7288 (tpt) cc_final: 0.6801 (tpt) REVERT: B 481 GLU cc_start: 0.2662 (tp30) cc_final: 0.2444 (tp30) REVERT: B 502 MET cc_start: 0.7262 (tpt) cc_final: 0.6754 (tpt) REVERT: C 481 GLU cc_start: 0.2675 (tp30) cc_final: 0.2465 (tp30) REVERT: C 502 MET cc_start: 0.7265 (tpt) cc_final: 0.6762 (tpt) REVERT: D 502 MET cc_start: 0.7280 (tpt) cc_final: 0.6776 (tpt) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.5474 time to fit residues: 112.1939 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 : 1.738 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.184578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127747 restraints weight = 28125.816| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.98 r_work: 0.3018 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3876 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= 0.122 Angle : 0.439 4.594 13288 Z= 0.239 Chirality : 0.037 0.137 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.887 20.563 1280 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.27 % Allowed : 8.53 % Favored : 90.20 % 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: 2.31 (0.25), residues: 1140 helix: 1.50 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 2.11 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 568 HIS 0.001 0.001 HIS C 402 PHE 0.010 0.001 PHE D 656 TYR 0.013 0.001 TYR B 616 ARG 0.003 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 680) hydrogen bonds : angle 3.74417 ( 2016) covalent geometry : bond 0.00269 ( 9776) covalent geometry : angle 0.43910 (13288) *********************** 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 169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7293 (tpt) cc_final: 0.6667 (tpt) REVERT: B 502 MET cc_start: 0.7274 (tpt) cc_final: 0.6654 (tpt) REVERT: C 502 MET cc_start: 0.7281 (tpt) cc_final: 0.6665 (tpt) REVERT: D 502 MET cc_start: 0.7304 (tpt) cc_final: 0.6687 (tpt) outliers start: 13 outliers final: 12 residues processed: 156 average time/residue: 0.5418 time to fit residues: 113.8492 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 : 1.532 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.179345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122131 restraints weight = 28742.260| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.01 r_work: 0.2949 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9776 Z= 0.248 Angle : 0.541 4.693 13288 Z= 0.302 Chirality : 0.041 0.137 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.165 20.735 1280 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.18 % Allowed : 8.92 % Favored : 89.90 % 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: 1.61 (0.25), residues: 1140 helix: 1.13 (0.16), residues: 904 sheet: None (None), residues: 0 loop : 1.29 (0.47), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 585 HIS 0.003 0.001 HIS C 402 PHE 0.014 0.002 PHE B 656 TYR 0.016 0.002 TYR C 616 ARG 0.004 0.001 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 680) hydrogen bonds : angle 4.01813 ( 2016) covalent geometry : bond 0.00582 ( 9776) covalent geometry : angle 0.54081 (13288) *********************** 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 : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7462 (tpt) cc_final: 0.6822 (tpt) REVERT: A 538 LYS cc_start: 0.7903 (mttt) cc_final: 0.7637 (mttt) REVERT: B 502 MET cc_start: 0.7418 (tpt) cc_final: 0.6782 (tpt) REVERT: B 538 LYS cc_start: 0.7916 (mttt) cc_final: 0.7653 (mttt) REVERT: C 502 MET cc_start: 0.7428 (tpt) cc_final: 0.6791 (tpt) REVERT: C 538 LYS cc_start: 0.7902 (mttt) cc_final: 0.7638 (mttt) REVERT: D 502 MET cc_start: 0.7446 (tpt) cc_final: 0.6810 (tpt) REVERT: D 538 LYS cc_start: 0.7914 (mttt) cc_final: 0.7647 (mttt) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.6481 time to fit residues: 123.2425 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 : 1.534 ------------------------------------------------------------------------------- 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 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 108 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.184772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128353 restraints weight = 28170.646| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.97 r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3953 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= 0.103 Angle : 0.431 4.592 13288 Z= 0.232 Chirality : 0.036 0.139 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.867 20.538 1280 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.88 % Allowed : 8.43 % Favored : 90.69 % 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: 1.52 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.90 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 568 HIS 0.001 0.000 HIS D 674 PHE 0.009 0.001 PHE A 656 TYR 0.012 0.001 TYR B 616 ARG 0.002 0.000 ARG D 537 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 680) hydrogen bonds : angle 3.73271 ( 2016) covalent geometry : bond 0.00217 ( 9776) covalent geometry : angle 0.43065 (13288) *********************** 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 157 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7343 (tpt) cc_final: 0.6820 (tpt) REVERT: B 462 MET cc_start: 0.7836 (ttm) cc_final: 0.7595 (ttm) REVERT: B 502 MET cc_start: 0.7289 (tpt) cc_final: 0.6777 (tpt) REVERT: C 462 MET cc_start: 0.7823 (ttm) cc_final: 0.7577 (ttm) REVERT: C 502 MET cc_start: 0.7295 (tpt) cc_final: 0.6779 (tpt) REVERT: D 462 MET cc_start: 0.7832 (ttm) cc_final: 0.7591 (ttm) REVERT: D 502 MET cc_start: 0.7328 (tpt) cc_final: 0.6818 (tpt) outliers start: 9 outliers final: 8 residues processed: 148 average time/residue: 0.6535 time to fit residues: 131.8792 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 : 2.286 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.184590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134664 restraints weight = 28323.932| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.88 r_work: 0.3208 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4069 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= 0.111 Angle : 0.432 4.548 13288 Z= 0.233 Chirality : 0.036 0.139 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.735 19.591 1280 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.18 % Allowed : 8.92 % Favored : 89.90 % 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: 2.51 (0.25), residues: 1140 helix: 1.70 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.91 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 568 HIS 0.001 0.000 HIS A 485 PHE 0.010 0.001 PHE A 656 TYR 0.014 0.001 TYR D 616 ARG 0.002 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 680) hydrogen bonds : angle 3.63754 ( 2016) covalent geometry : bond 0.00240 ( 9776) covalent geometry : angle 0.43228 (13288) ********************** 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 154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 MET cc_start: 0.7314 (tpt) cc_final: 0.6676 (tpt) REVERT: B 462 MET cc_start: 0.7812 (ttm) cc_final: 0.7543 (ttm) REVERT: B 502 MET cc_start: 0.7282 (tpt) cc_final: 0.6656 (tpt) REVERT: C 462 MET cc_start: 0.7795 (ttm) cc_final: 0.7522 (ttm) REVERT: C 502 MET cc_start: 0.7272 (tpt) cc_final: 0.6643 (tpt) REVERT: D 462 MET cc_start: 0.7801 (ttm) cc_final: 0.7531 (ttm) REVERT: D 502 MET cc_start: 0.7289 (tpt) cc_final: 0.6660 (tpt) outliers start: 12 outliers final: 12 residues processed: 142 average time/residue: 0.5907 time to fit residues: 112.3360 Evaluate side-chains 154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.184352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127016 restraints weight = 28295.151| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.03 r_work: 0.3114 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4059 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= 0.125 Angle : 0.441 4.594 13288 Z= 0.238 Chirality : 0.037 0.138 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.732 19.385 1280 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.88 % Allowed : 8.82 % Favored : 90.29 % 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: 2.46 (0.25), residues: 1140 helix: 1.66 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 1.88 (0.49), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 568 HIS 0.002 0.001 HIS B 674 PHE 0.010 0.001 PHE B 656 TYR 0.014 0.001 TYR C 616 ARG 0.002 0.000 ARG B 679 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 680) hydrogen bonds : angle 3.65866 ( 2016) covalent geometry : bond 0.00277 ( 9776) covalent geometry : angle 0.44068 (13288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10638.36 seconds wall clock time: 186 minutes 26.88 seconds (11186.88 seconds total)