Starting phenix.real_space_refine on Tue Aug 4 21:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymc_73102/08_2026/9ymc_73102.map" } resolution = 3.28 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= 0.009 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 P 20 5.49 5 S 40 5.16 5 C 4087 2.51 5 N 1177 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 5} Chain: "A" Number of atoms: 6134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 6134 Classifications: {'peptide': 768} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 721} Chain breaks: 4 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 258 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain breaks: 1 Time building chain proxies: 1.28, per 1000 atoms: 0.20 Number of scatterers: 6559 At special positions: 0 Unit cell: (76.82, 85.17, 106.88, 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 40 16.00 P 20 15.00 O 1235 8.00 N 1177 7.00 C 4087 6.00 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: 0.45 Conformation dependent library (CDL) restraints added in 303.3 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 34.9% alpha, 15.8% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 67 through 83 removed outlier: 4.461A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.900A pdb=" N LEU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.799A pdb=" N LYS A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.590A pdb=" N THR A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 385 removed outlier: 4.158A pdb=" N GLU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 398 removed outlier: 3.649A pdb=" N ARG A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.502A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.415A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.659A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.619A pdb=" N LEU A 560 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.013A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 605 removed outlier: 4.011A pdb=" N GLY A 604 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 removed outlier: 3.583A pdb=" N VAL A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.852A pdb=" N HIS A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 682 " --> pdb=" O GLN A 678 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 817 removed outlier: 3.660A pdb=" N ARG A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.907A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.341A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 707 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 592 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N TYR A 667 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU A 594 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 207 removed outlier: 3.589A pdb=" N ARG A 207 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 400 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.576A pdb=" N VAL A 93 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 102 " --> pdb=" O TYR A 55 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 136 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 280 removed outlier: 3.874A pdb=" N ARG A 277 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.640A pdb=" N ASN A 283 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 428 removed outlier: 3.771A pdb=" N ILE A 577 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 452 removed outlier: 5.734A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 597 through 599 removed outlier: 3.694A pdb=" N ILE A 611 " --> pdb=" O THR A 599 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1987 1.34 - 1.45: 1031 1.45 - 1.57: 3633 1.57 - 1.69: 37 1.69 - 1.81: 59 Bond restraints: 6747 Sorted by residual: bond pdb=" N GLY A 121 " pdb=" CA GLY A 121 " ideal model delta sigma weight residual 1.445 1.478 -0.033 9.90e-03 1.02e+04 1.12e+01 bond pdb=" P A B 22 " pdb=" O5' A B 22 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 8.87e+00 bond pdb=" N LYS A 124 " pdb=" CA LYS A 124 " ideal model delta sigma weight residual 1.458 1.485 -0.028 1.12e-02 7.97e+03 6.03e+00 bond pdb=" N GLU A 122 " pdb=" CA GLU A 122 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.03e+00 bond pdb=" N ASP A 125 " pdb=" CA ASP A 125 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.91e+00 ... (remaining 6742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8844 1.62 - 3.23: 319 3.23 - 4.85: 43 4.85 - 6.47: 8 6.47 - 8.09: 4 Bond angle restraints: 9218 Sorted by residual: angle pdb=" C4' G B 23 " pdb=" O4' G B 23 " pdb=" C1' G B 23 " ideal model delta sigma weight residual 109.70 106.13 3.57 7.00e-01 2.04e+00 2.60e+01 angle pdb=" N GLY A 123 " pdb=" CA GLY A 123 " pdb=" C GLY A 123 " ideal model delta sigma weight residual 115.40 109.11 6.29 1.32e+00 5.74e-01 2.27e+01 angle pdb=" C3' U B 21 " pdb=" O3' U B 21 " pdb=" P A B 22 " ideal model delta sigma weight residual 119.70 125.12 -5.42 1.20e+00 6.94e-01 2.04e+01 angle pdb=" O3' U B 21 " pdb=" P A B 22 " pdb=" O5' A B 22 " ideal model delta sigma weight residual 104.00 111.32 -7.32 1.90e+00 2.77e-01 1.48e+01 angle pdb=" N GLY A 331 " pdb=" CA GLY A 331 " pdb=" C GLY A 331 " ideal model delta sigma weight residual 111.56 115.32 -3.76 1.01e+00 9.80e-01 1.38e+01 ... (remaining 9213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 3854 24.55 - 49.10: 185 49.10 - 73.65: 65 73.65 - 98.20: 10 98.20 - 122.75: 1 Dihedral angle restraints: 4115 sinusoidal: 1882 harmonic: 2233 Sorted by residual: dihedral pdb=" C5' G B 23 " pdb=" C4' G B 23 " pdb=" C3' G B 23 " pdb=" O3' G B 23 " ideal model delta sinusoidal sigma weight residual 147.00 96.75 50.25 1 8.00e+00 1.56e-02 5.41e+01 dihedral pdb=" O4' G B 23 " pdb=" C4' G B 23 " pdb=" C3' G B 23 " pdb=" C2' G B 23 " ideal model delta sinusoidal sigma weight residual 24.00 -21.57 45.57 1 8.00e+00 1.56e-02 4.50e+01 dihedral pdb=" C3' G B 23 " pdb=" C4' G B 23 " pdb=" O4' G B 23 " pdb=" C1' G B 23 " ideal model delta sinusoidal sigma weight residual -2.00 38.53 -40.53 1 8.00e+00 1.56e-02 3.60e+01 ... (remaining 4112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1012 0.121 - 0.241: 26 0.241 - 0.361: 1 0.361 - 0.482: 0 0.482 - 0.602: 2 Chirality restraints: 1041 Sorted by residual: chirality pdb=" P A B 22 " pdb=" OP1 A B 22 " pdb=" OP2 A B 22 " pdb=" O5' A B 22 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" P U B 21 " pdb=" OP1 U B 21 " pdb=" OP2 U B 21 " pdb=" O5' U B 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" P G B 23 " pdb=" OP1 G B 23 " pdb=" OP2 G B 23 " pdb=" O5' G B 23 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1038 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 126 " 0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG A 126 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 126 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 126 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 126 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 23 " -0.030 2.00e-02 2.50e+03 1.54e-02 5.36e+00 pdb=" N1 U C 23 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U C 23 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U C 23 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U C 23 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U C 23 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U C 23 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U C 23 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U C 23 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 19 " -0.027 2.00e-02 2.50e+03 1.24e-02 4.65e+00 pdb=" N9 G C 19 " 0.033 2.00e-02 2.50e+03 pdb=" C8 G C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G C 19 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G C 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G C 19 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G C 19 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G C 19 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 19 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 702 2.75 - 3.28: 6477 3.28 - 3.82: 10564 3.82 - 4.36: 12528 4.36 - 4.90: 21594 Nonbonded interactions: 51865 Sorted by model distance: nonbonded pdb=" NH1 ARG A 668 " pdb=" O ASP A 669 " model vdw 2.208 3.120 nonbonded pdb=" ND2 ASN A 729 " pdb=" O GLY A 758 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 703 " pdb=" OD1 ASN A 772 " model vdw 2.240 3.040 nonbonded pdb=" O ARG A 167 " pdb=" OG SER A 171 " model vdw 2.253 3.040 nonbonded pdb=" O ASN A 359 " pdb=" OG1 THR A 363 " model vdw 2.255 3.040 ... (remaining 51860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 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 : 0.004 0.058 6747 Z= 0.214 Angle : 0.706 8.086 9218 Z= 0.448 Chirality : 0.055 0.602 1041 Planarity : 0.006 0.121 1116 Dihedral : 16.195 122.750 2669 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.55 % Allowed : 8.86 % Favored : 87.59 % 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 are not related in a simple way. whole: -1.61 (0.30), residues: 758 helix: -0.28 (0.35), residues: 215 sheet: -1.60 (0.37), residues: 170 loop : -1.18 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.012 0.001 TYR A 101 PHE 0.013 0.002 PHE A 666 TRP 0.011 0.001 TRP A 435 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.21 ( 6747) covalent geometry : angle 0.70614 / 0.45 ( 9218) hydrogen bonds : bond 0.21173 / 21.96 ( 242) hydrogen bonds : angle 8.42468 / 7.68 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.229 Fit side-chains REVERT: A 30 ASP cc_start: 0.6915 (t0) cc_final: 0.6449 (t0) REVERT: A 47 MET cc_start: 0.6957 (ttp) cc_final: 0.6475 (ttt) REVERT: A 212 LYS cc_start: 0.8156 (pttm) cc_final: 0.7580 (ptmt) REVERT: A 225 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4155 (m-80) REVERT: A 338 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: A 399 ILE cc_start: 0.7303 (mt) cc_final: 0.7003 (mt) REVERT: A 402 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7592 (mmmt) REVERT: A 483 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8226 (ppp) REVERT: A 634 HIS cc_start: 0.6648 (t70) cc_final: 0.6132 (t-90) REVERT: A 635 ARG cc_start: 0.8124 (mmt180) cc_final: 0.6996 (tpt170) REVERT: A 726 LYS cc_start: 0.6385 (mttt) cc_final: 0.6176 (ttpt) REVERT: A 811 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: A 812 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6871 (ttm-80) outliers start: 24 outliers final: 11 residues processed: 117 average time/residue: 0.0889 time to fit residues: 13.7492 Evaluate side-chains 97 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.206818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.167792 restraints weight = 8620.946| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.38 r_work: 0.4045 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6747 Z= 0.139 Angle : 0.622 5.162 9218 Z= 0.333 Chirality : 0.047 0.216 1041 Planarity : 0.005 0.068 1116 Dihedral : 15.631 127.283 1164 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.99 % Allowed : 11.08 % Favored : 84.93 % 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 are not related in a simple way. whole: -1.35 (0.30), residues: 758 helix: -0.19 (0.34), residues: 232 sheet: -1.18 (0.38), residues: 173 loop : -1.11 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.011 0.001 TYR A 420 PHE 0.012 0.002 PHE A 666 TRP 0.008 0.001 TRP A 451 HIS 0.005 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6747) covalent geometry : angle 0.62228 / 0.33 ( 9218) hydrogen bonds : bond 0.05258 / 5.12 ( 242) hydrogen bonds : angle 6.18607 / 5.46 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.236 Fit side-chains REVERT: A 47 MET cc_start: 0.7115 (ttp) cc_final: 0.6759 (ttt) REVERT: A 48 ASP cc_start: 0.6144 (t0) cc_final: 0.5712 (p0) REVERT: A 192 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.6906 (mp) REVERT: A 212 LYS cc_start: 0.8257 (pttm) cc_final: 0.7645 (ptmt) REVERT: A 214 MET cc_start: 0.7815 (mtt) cc_final: 0.7537 (mtt) REVERT: A 225 TYR cc_start: 0.5293 (OUTLIER) cc_final: 0.4264 (m-80) REVERT: A 338 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: A 365 ILE cc_start: 0.7692 (mp) cc_final: 0.7239 (tp) REVERT: A 402 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7547 (mmmt) REVERT: A 483 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7677 (ppp) REVERT: A 634 HIS cc_start: 0.6574 (t70) cc_final: 0.6096 (t-90) REVERT: A 635 ARG cc_start: 0.8196 (mmt180) cc_final: 0.6972 (tpt170) REVERT: A 811 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: A 812 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.5876 (ttm-80) outliers start: 27 outliers final: 19 residues processed: 113 average time/residue: 0.0895 time to fit residues: 13.3739 Evaluate side-chains 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.204814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165695 restraints weight = 8553.536| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.34 r_work: 0.4034 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6747 Z= 0.158 Angle : 0.618 6.942 9218 Z= 0.329 Chirality : 0.046 0.222 1041 Planarity : 0.005 0.076 1116 Dihedral : 15.532 124.688 1164 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.87 % Allowed : 11.67 % Favored : 83.46 % 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 are not related in a simple way. whole: -1.43 (0.30), residues: 758 helix: -0.22 (0.34), residues: 230 sheet: -1.32 (0.39), residues: 174 loop : -1.13 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 395 TYR 0.012 0.001 TYR A 55 PHE 0.018 0.002 PHE A 666 TRP 0.009 0.001 TRP A 451 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6747) covalent geometry : angle 0.61847 / 0.33 ( 9218) hydrogen bonds : bond 0.04814 / 4.70 ( 242) hydrogen bonds : angle 5.92870 / 5.30 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7203 (ttp) cc_final: 0.6853 (ttt) REVERT: A 48 ASP cc_start: 0.6222 (t0) cc_final: 0.5754 (p0) REVERT: A 186 GLU cc_start: 0.4858 (OUTLIER) cc_final: 0.4248 (pm20) REVERT: A 212 LYS cc_start: 0.8328 (pttm) cc_final: 0.7712 (ptmt) REVERT: A 225 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4348 (m-80) REVERT: A 338 TYR cc_start: 0.7308 (m-80) cc_final: 0.6953 (m-80) REVERT: A 346 ILE cc_start: 0.6227 (OUTLIER) cc_final: 0.5864 (mp) REVERT: A 365 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7181 (tp) REVERT: A 402 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7677 (mmmm) REVERT: A 483 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7802 (ppp) REVERT: A 619 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: A 634 HIS cc_start: 0.6754 (t70) cc_final: 0.6263 (t-90) REVERT: A 635 ARG cc_start: 0.8284 (mmt180) cc_final: 0.6993 (tpt170) REVERT: A 811 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: A 812 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.5904 (ttm-80) outliers start: 33 outliers final: 21 residues processed: 114 average time/residue: 0.0919 time to fit residues: 13.8050 Evaluate side-chains 117 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.207088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168588 restraints weight = 8591.214| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.36 r_work: 0.4037 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6747 Z= 0.120 Angle : 0.571 6.745 9218 Z= 0.302 Chirality : 0.045 0.208 1041 Planarity : 0.005 0.072 1116 Dihedral : 15.350 122.933 1162 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.87 % Allowed : 13.88 % Favored : 81.24 % 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 are not related in a simple way. whole: -1.24 (0.30), residues: 758 helix: -0.03 (0.34), residues: 230 sheet: -1.21 (0.39), residues: 173 loop : -1.05 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.010 0.001 TYR A 55 PHE 0.018 0.002 PHE A 746 TRP 0.010 0.001 TRP A 451 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6747) covalent geometry : angle 0.57104 / 0.30 ( 9218) hydrogen bonds : bond 0.04155 / 4.05 ( 242) hydrogen bonds : angle 5.68514 / 5.16 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7122 (ttp) cc_final: 0.6857 (ttt) REVERT: A 48 ASP cc_start: 0.6207 (t0) cc_final: 0.5669 (p0) REVERT: A 169 LEU cc_start: 0.4593 (OUTLIER) cc_final: 0.4312 (tp) REVERT: A 186 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4267 (pm20) REVERT: A 212 LYS cc_start: 0.8287 (pttm) cc_final: 0.7615 (ptmt) REVERT: A 225 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.4484 (m-80) REVERT: A 338 TYR cc_start: 0.7330 (m-80) cc_final: 0.7037 (m-80) REVERT: A 346 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5868 (mp) REVERT: A 402 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7621 (mmmm) REVERT: A 619 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: A 634 HIS cc_start: 0.6715 (t70) cc_final: 0.6240 (t-90) REVERT: A 635 ARG cc_start: 0.8267 (mmt180) cc_final: 0.6957 (tpt170) REVERT: A 658 ARG cc_start: 0.8276 (mpt-90) cc_final: 0.8072 (mmm160) REVERT: A 659 PHE cc_start: 0.8459 (m-10) cc_final: 0.8200 (m-10) REVERT: A 811 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: A 812 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.5841 (ttm-80) outliers start: 33 outliers final: 21 residues processed: 124 average time/residue: 0.0820 time to fit residues: 13.8223 Evaluate side-chains 118 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN A 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.207159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168404 restraints weight = 8754.205| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.40 r_work: 0.4032 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6747 Z= 0.125 Angle : 0.581 6.813 9218 Z= 0.304 Chirality : 0.045 0.198 1041 Planarity : 0.005 0.059 1116 Dihedral : 15.193 121.191 1158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.17 % Allowed : 14.03 % Favored : 80.80 % 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 are not related in a simple way. whole: -1.24 (0.30), residues: 758 helix: 0.01 (0.34), residues: 230 sheet: -1.42 (0.38), residues: 179 loop : -0.92 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.009 0.001 TYR A 55 PHE 0.014 0.001 PHE A 746 TRP 0.010 0.001 TRP A 451 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6747) covalent geometry : angle 0.58127 / 0.30 ( 9218) hydrogen bonds : bond 0.03966 / 3.88 ( 242) hydrogen bonds : angle 5.56049 / 5.08 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.298 Fit side-chains REVERT: A 47 MET cc_start: 0.7205 (ttp) cc_final: 0.6947 (ttt) REVERT: A 48 ASP cc_start: 0.6272 (t0) cc_final: 0.5544 (p0) REVERT: A 82 PHE cc_start: 0.4668 (m-80) cc_final: 0.4465 (m-80) REVERT: A 169 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4328 (tp) REVERT: A 186 GLU cc_start: 0.4833 (OUTLIER) cc_final: 0.4232 (pm20) REVERT: A 212 LYS cc_start: 0.8299 (pttm) cc_final: 0.7445 (ptmm) REVERT: A 214 MET cc_start: 0.7739 (mtt) cc_final: 0.7539 (mtt) REVERT: A 225 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.4547 (m-80) REVERT: A 346 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5883 (mp) REVERT: A 365 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7044 (tp) REVERT: A 402 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7610 (mmmm) REVERT: A 446 ILE cc_start: 0.7476 (mp) cc_final: 0.7122 (tt) REVERT: A 619 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 634 HIS cc_start: 0.6733 (t70) cc_final: 0.6231 (t-90) REVERT: A 635 ARG cc_start: 0.8227 (mmt180) cc_final: 0.6974 (tpt170) REVERT: A 811 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: A 812 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.5791 (ttm-80) outliers start: 35 outliers final: 25 residues processed: 119 average time/residue: 0.1000 time to fit residues: 15.5536 Evaluate side-chains 120 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.207882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.168912 restraints weight = 8659.167| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.41 r_work: 0.4038 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6747 Z= 0.119 Angle : 0.570 7.429 9218 Z= 0.297 Chirality : 0.044 0.185 1041 Planarity : 0.005 0.079 1116 Dihedral : 15.117 119.291 1157 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.47 % Allowed : 14.48 % Favored : 80.06 % 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 are not related in a simple way. whole: -1.15 (0.31), residues: 758 helix: 0.08 (0.34), residues: 235 sheet: -1.40 (0.38), residues: 179 loop : -0.86 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.009 0.001 TYR A 55 PHE 0.014 0.001 PHE A 659 TRP 0.010 0.001 TRP A 451 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6747) covalent geometry : angle 0.56975 / 0.30 ( 9218) hydrogen bonds : bond 0.03816 / 3.71 ( 242) hydrogen bonds : angle 5.42747 / 4.99 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.237 Fit side-chains REVERT: A 48 ASP cc_start: 0.6299 (t0) cc_final: 0.6058 (m-30) REVERT: A 82 PHE cc_start: 0.4660 (m-80) cc_final: 0.4454 (m-80) REVERT: A 169 LEU cc_start: 0.4432 (OUTLIER) cc_final: 0.4203 (tp) REVERT: A 186 GLU cc_start: 0.4806 (OUTLIER) cc_final: 0.4221 (pm20) REVERT: A 214 MET cc_start: 0.7747 (mtt) cc_final: 0.7531 (mtt) REVERT: A 225 TYR cc_start: 0.5561 (OUTLIER) cc_final: 0.4482 (m-80) REVERT: A 346 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.5907 (mp) REVERT: A 400 MET cc_start: 0.6600 (mmm) cc_final: 0.5492 (ptp) REVERT: A 402 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7643 (mmmm) REVERT: A 446 ILE cc_start: 0.7482 (mp) cc_final: 0.7135 (tt) REVERT: A 483 MET cc_start: 0.7737 (ppp) cc_final: 0.7435 (ppp) REVERT: A 619 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: A 634 HIS cc_start: 0.6703 (t70) cc_final: 0.6209 (t-90) REVERT: A 635 ARG cc_start: 0.8208 (mmt180) cc_final: 0.6956 (tpt170) REVERT: A 811 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: A 812 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.5764 (ttm-80) outliers start: 37 outliers final: 27 residues processed: 120 average time/residue: 0.0859 time to fit residues: 13.7594 Evaluate side-chains 119 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 788 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.202350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165883 restraints weight = 8613.569| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.31 r_work: 0.3975 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6747 Z= 0.197 Angle : 0.662 8.019 9218 Z= 0.345 Chirality : 0.047 0.173 1041 Planarity : 0.006 0.083 1116 Dihedral : 15.200 117.312 1157 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.76 % Allowed : 14.77 % Favored : 79.47 % 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 are not related in a simple way. whole: -1.55 (0.30), residues: 758 helix: -0.33 (0.33), residues: 238 sheet: -1.60 (0.38), residues: 175 loop : -1.07 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 286 TYR 0.013 0.002 TYR A 101 PHE 0.021 0.002 PHE A 666 TRP 0.012 0.001 TRP A 451 HIS 0.008 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 6747) covalent geometry : angle 0.66173 / 0.34 ( 9218) hydrogen bonds : bond 0.04429 / 4.33 ( 242) hydrogen bonds : angle 5.72607 / 5.14 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6185 (t0) cc_final: 0.5957 (m-30) REVERT: A 82 PHE cc_start: 0.4757 (m-80) cc_final: 0.4532 (m-80) REVERT: A 186 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.3983 (pm20) REVERT: A 214 MET cc_start: 0.7912 (mtt) cc_final: 0.7687 (mtt) REVERT: A 346 ILE cc_start: 0.6358 (OUTLIER) cc_final: 0.5977 (mp) REVERT: A 400 MET cc_start: 0.6756 (mmm) cc_final: 0.5764 (ptp) REVERT: A 402 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7649 (mmmm) REVERT: A 619 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: A 634 HIS cc_start: 0.6832 (t70) cc_final: 0.6318 (t-90) REVERT: A 635 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7036 (tpt170) REVERT: A 811 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: A 812 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.5804 (ttm-80) outliers start: 39 outliers final: 27 residues processed: 117 average time/residue: 0.0830 time to fit residues: 12.8159 Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.205610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.169825 restraints weight = 8619.898| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.34 r_work: 0.4011 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6747 Z= 0.132 Angle : 0.624 9.288 9218 Z= 0.322 Chirality : 0.045 0.184 1041 Planarity : 0.005 0.085 1116 Dihedral : 15.108 115.110 1157 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.02 % Allowed : 15.51 % Favored : 79.47 % 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 are not related in a simple way. whole: -1.34 (0.31), residues: 758 helix: -0.11 (0.34), residues: 238 sheet: -1.44 (0.38), residues: 174 loop : -1.02 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.009 0.001 TYR A 55 PHE 0.024 0.002 PHE A 676 TRP 0.012 0.001 TRP A 451 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6747) covalent geometry : angle 0.62361 / 0.32 ( 9218) hydrogen bonds : bond 0.03980 / 3.88 ( 242) hydrogen bonds : angle 5.54866 / 5.04 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6117 (t0) cc_final: 0.5827 (m-30) REVERT: A 82 PHE cc_start: 0.4802 (m-80) cc_final: 0.4559 (m-80) REVERT: A 186 GLU cc_start: 0.4865 (OUTLIER) cc_final: 0.4224 (pm20) REVERT: A 214 MET cc_start: 0.7876 (mtt) cc_final: 0.7664 (mtt) REVERT: A 346 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.5851 (mp) REVERT: A 400 MET cc_start: 0.6721 (mmm) cc_final: 0.5968 (ptp) REVERT: A 402 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7636 (mmmm) REVERT: A 437 MET cc_start: 0.5892 (mmm) cc_final: 0.5298 (mtt) REVERT: A 619 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8055 (m-30) REVERT: A 634 HIS cc_start: 0.6859 (t70) cc_final: 0.6336 (t-90) REVERT: A 635 ARG cc_start: 0.8318 (mmt180) cc_final: 0.7037 (tpt170) REVERT: A 811 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6419 (m-80) outliers start: 34 outliers final: 28 residues processed: 109 average time/residue: 0.0853 time to fit residues: 12.5177 Evaluate side-chains 113 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.206197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167519 restraints weight = 8579.340| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.41 r_work: 0.4049 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6747 Z= 0.124 Angle : 0.597 8.993 9218 Z= 0.309 Chirality : 0.045 0.183 1041 Planarity : 0.005 0.074 1116 Dihedral : 14.960 112.192 1157 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.02 % Allowed : 15.21 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.31), residues: 758 helix: -0.04 (0.34), residues: 238 sheet: -1.41 (0.38), residues: 179 loop : -0.91 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.008 0.001 TYR A 55 PHE 0.019 0.002 PHE A 676 TRP 0.010 0.001 TRP A 451 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6747) covalent geometry : angle 0.59728 / 0.31 ( 9218) hydrogen bonds : bond 0.03765 / 3.71 ( 242) hydrogen bonds : angle 5.36216 / 4.96 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6023 (t0) cc_final: 0.5699 (m-30) REVERT: A 82 PHE cc_start: 0.4945 (m-80) cc_final: 0.4678 (m-80) REVERT: A 129 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7196 (mtpp) REVERT: A 186 GLU cc_start: 0.4718 (OUTLIER) cc_final: 0.4127 (pm20) REVERT: A 214 MET cc_start: 0.7765 (mtt) cc_final: 0.7557 (mtt) REVERT: A 346 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5822 (mp) REVERT: A 400 MET cc_start: 0.6883 (mmm) cc_final: 0.6135 (ptp) REVERT: A 402 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7578 (mmmm) REVERT: A 619 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: A 634 HIS cc_start: 0.6778 (t70) cc_final: 0.6251 (t-90) REVERT: A 635 ARG cc_start: 0.8179 (mmt180) cc_final: 0.6999 (tpt170) REVERT: A 811 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 812 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6710 (ttm-80) outliers start: 34 outliers final: 27 residues processed: 115 average time/residue: 0.0837 time to fit residues: 12.8934 Evaluate side-chains 119 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.207346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.168014 restraints weight = 8575.107| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.43 r_work: 0.4032 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6747 Z= 0.125 Angle : 0.613 9.909 9218 Z= 0.315 Chirality : 0.044 0.163 1041 Planarity : 0.005 0.079 1116 Dihedral : 14.946 110.465 1157 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.02 % Allowed : 16.25 % Favored : 78.73 % 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 are not related in a simple way. whole: -1.24 (0.31), residues: 758 helix: -0.11 (0.34), residues: 237 sheet: -1.41 (0.37), residues: 184 loop : -0.82 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 395 TYR 0.010 0.001 TYR A 55 PHE 0.019 0.002 PHE A 676 TRP 0.010 0.001 TRP A 451 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6747) covalent geometry : angle 0.61292 / 0.31 ( 9218) hydrogen bonds : bond 0.03739 / 3.72 ( 242) hydrogen bonds : angle 5.31230 / 4.95 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 82 PHE cc_start: 0.4955 (m-80) cc_final: 0.4692 (m-80) REVERT: A 129 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7146 (mtpp) REVERT: A 186 GLU cc_start: 0.4704 (OUTLIER) cc_final: 0.4125 (pm20) REVERT: A 214 MET cc_start: 0.7779 (mtt) cc_final: 0.7575 (mtt) REVERT: A 346 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.5895 (mp) REVERT: A 400 MET cc_start: 0.6899 (mmm) cc_final: 0.6207 (mtm) REVERT: A 402 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7478 (mmmm) REVERT: A 446 ILE cc_start: 0.7495 (mp) cc_final: 0.7071 (tt) REVERT: A 619 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: A 634 HIS cc_start: 0.6816 (t70) cc_final: 0.6298 (t-90) REVERT: A 635 ARG cc_start: 0.8144 (mmt180) cc_final: 0.6977 (tpt170) REVERT: A 778 GLU cc_start: 0.7876 (tp30) cc_final: 0.7574 (tp30) REVERT: A 812 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6728 (ttm-80) outliers start: 34 outliers final: 28 residues processed: 114 average time/residue: 0.0855 time to fit residues: 13.0557 Evaluate side-chains 119 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.170692 restraints weight = 8546.437| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.29 r_work: 0.4023 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6747 Z= 0.135 Angle : 0.605 9.843 9218 Z= 0.311 Chirality : 0.045 0.163 1041 Planarity : 0.005 0.074 1116 Dihedral : 14.833 108.410 1155 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.02 % Allowed : 16.25 % Favored : 78.73 % 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 are not related in a simple way. whole: -1.28 (0.31), residues: 758 helix: -0.13 (0.34), residues: 237 sheet: -1.42 (0.37), residues: 180 loop : -0.88 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.009 0.001 TYR A 55 PHE 0.019 0.002 PHE A 676 TRP 0.010 0.001 TRP A 451 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6747) covalent geometry : angle 0.60530 / 0.31 ( 9218) hydrogen bonds : bond 0.03771 / 3.72 ( 242) hydrogen bonds : angle 5.32677 / 4.96 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.41 seconds wall clock time: 31 minutes 23.99 seconds (1883.99 seconds total)