Starting phenix.real_space_refine on Thu Jul 2 05:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymc_73102/07_2026/9ymc_73102.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymc_73102/07_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_73102/07_2026/9ymc_73102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymc_73102/07_2026/9ymc_73102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymc_73102/07_2026/9ymc_73102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymc_73102/07_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-dev-6108/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: 1.77, per 1000 atoms: 0.27 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: 0.62 Conformation dependent library (CDL) restraints added in 388.9 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: 0.56 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: 0.98 Time building geometry restraints manager: 0.82 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=" O5' A B 22 " pdb=" C5' A B 22 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.36e+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: 8885 1.62 - 3.23: 277 3.23 - 4.85: 44 4.85 - 6.47: 8 6.47 - 8.09: 4 Bond angle restraints: 9218 Sorted by residual: 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 1.50e+00 4.44e-01 2.38e+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=" 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 angle pdb=" C1' U C 23 " pdb=" N1 U C 23 " pdb=" C2 U C 23 " ideal model delta sigma weight residual 117.70 122.09 -4.39 1.20e+00 6.94e-01 1.34e+01 angle pdb=" CA GLY A 121 " pdb=" C GLY A 121 " pdb=" O GLY A 121 " ideal model delta sigma weight residual 121.57 117.72 3.85 1.07e+00 8.73e-01 1.29e+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: 1025 0.121 - 0.241: 13 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: 2.410 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.160 Find NCS groups from input model: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- 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= 0.206 Angle : 0.688 8.086 9218 Z= 0.424 Chirality : 0.053 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 0.00380 / 0.21 ( 6747) covalent geometry : angle 0.68825 / 0.42 ( 9218) hydrogen bonds : bond 0.21173 / 20.62 ( 242) hydrogen bonds : angle 8.42468 / 7.31 ( 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 : 0.168 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: 0.4156 (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: 0.0891 time to fit residues: 13.4388 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 : 0.226 ------------------------------------------------------------------------------- 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 A 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.167540 restraints weight = 8616.504| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 3.37 r_work: 0.4043 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6747 Z= 0.141 Angle : 0.618 5.047 9218 Z= 0.334 Chirality : 0.046 0.180 1041 Planarity : 0.005 0.071 1116 Dihedral : 15.609 125.847 1164 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.99 % Allowed : 10.78 % Favored : 85.23 % 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 (0.30), residues: 758 helix: -0.19 (0.34), residues: 232 sheet: -1.18 (0.38), residues: 173 loop : -1.10 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.010 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 0.00295 / 0.14 ( 6747) covalent geometry : angle 0.61833 / 0.33 ( 9218) hydrogen bonds : bond 0.05569 / 4.94 ( 242) hydrogen bonds : angle 6.26692 / 5.22 ( 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 124 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.238 Fit side-chains REVERT: A 47 MET cc_start: 0.7158 (ttp) cc_final: 0.6784 (ttt) REVERT: A 48 ASP cc_start: 0.6140 (t0) cc_final: 0.5733 (p0) REVERT: A 192 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.6893 (mp) REVERT: A 212 LYS cc_start: 0.8261 (pttm) cc_final: 0.7666 (ptmt) REVERT: A 225 TYR cc_start: 0.5293 (OUTLIER) cc_final: 0.4248 (m-80) REVERT: A 365 ILE cc_start: 0.7708 (mp) cc_final: 0.7135 (tp) REVERT: A 402 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7556 (mmmt) REVERT: A 483 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7715 (ppp) REVERT: A 634 HIS cc_start: 0.6576 (t70) cc_final: 0.6069 (t-90) REVERT: A 635 ARG cc_start: 0.8196 (mmt180) cc_final: 0.6966 (tpt170) REVERT: A 726 LYS cc_start: 0.6340 (mttt) cc_final: 0.6139 (ttpt) REVERT: A 811 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: A 812 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.5856 (ttm-80) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 0.0870 time to fit residues: 13.0911 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 119 LEU 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 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: 2.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.206850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.167853 restraints weight = 8564.264| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.37 r_work: 0.4046 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6747 Z= 0.131 Angle : 0.596 6.108 9218 Z= 0.318 Chirality : 0.045 0.157 1041 Planarity : 0.005 0.072 1116 Dihedral : 15.422 123.817 1162 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.43 % Allowed : 11.67 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.30), residues: 758 helix: -0.12 (0.34), residues: 233 sheet: -1.27 (0.38), residues: 174 loop : -1.09 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.019 0.001 TYR A 338 PHE 0.014 0.002 PHE A 666 TRP 0.008 0.001 TRP A 451 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6747) covalent geometry : angle 0.59646 / 0.32 ( 9218) hydrogen bonds : bond 0.04656 / 4.08 ( 242) hydrogen bonds : angle 5.88391 / 4.97 ( 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 130 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.228 Fit side-chains REVERT: A 47 MET cc_start: 0.7163 (ttp) cc_final: 0.6789 (ttt) REVERT: A 48 ASP cc_start: 0.6213 (t0) cc_final: 0.5760 (p0) REVERT: A 186 GLU cc_start: 0.4810 (OUTLIER) cc_final: 0.4267 (pm20) REVERT: A 212 LYS cc_start: 0.8305 (pttm) cc_final: 0.7667 (ptmt) REVERT: A 225 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.4348 (m-80) REVERT: A 346 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5833 (mp) REVERT: A 365 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7257 (tp) REVERT: A 402 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7658 (mmmm) REVERT: A 551 ASN cc_start: 0.5475 (m-40) cc_final: 0.4983 (m-40) REVERT: A 619 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 634 HIS cc_start: 0.6679 (t70) cc_final: 0.6193 (t-90) REVERT: A 635 ARG cc_start: 0.8213 (mmt180) cc_final: 0.6954 (tpt170) REVERT: A 811 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: A 812 ARG cc_start: 0.7127 (mmm-85) cc_final: 0.5875 (ttm-80) outliers start: 30 outliers final: 19 residues processed: 118 average time/residue: 0.0937 time to fit residues: 14.2544 Evaluate side-chains 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 508 LEU Chi-restraints excluded: chain A residue 559 THR 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.208539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170268 restraints weight = 8601.710| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 3.39 r_work: 0.4055 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6747 Z= 0.115 Angle : 0.572 6.732 9218 Z= 0.302 Chirality : 0.045 0.146 1041 Planarity : 0.005 0.072 1116 Dihedral : 15.249 122.075 1158 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.58 % Allowed : 13.74 % Favored : 81.68 % 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: -1.19 (0.30), residues: 758 helix: 0.06 (0.34), residues: 233 sheet: -1.27 (0.38), residues: 178 loop : -0.98 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.020 0.001 TYR A 338 PHE 0.019 0.001 PHE A 746 TRP 0.009 0.001 TRP A 451 HIS 0.003 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 6747) covalent geometry : angle 0.57167 / 0.30 ( 9218) hydrogen bonds : bond 0.04063 / 3.55 ( 242) hydrogen bonds : angle 5.61792 / 4.81 ( 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 132 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.226 Fit side-chains REVERT: A 47 MET cc_start: 0.7092 (ttp) cc_final: 0.6840 (ttt) REVERT: A 48 ASP cc_start: 0.6186 (t0) cc_final: 0.5684 (p0) REVERT: A 169 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4371 (tp) REVERT: A 186 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.4290 (pm20) REVERT: A 212 LYS cc_start: 0.8268 (pttm) cc_final: 0.7631 (ptmt) REVERT: A 225 TYR cc_start: 0.5458 (OUTLIER) cc_final: 0.4477 (m-80) REVERT: A 346 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5872 (mp) REVERT: A 402 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7641 (mmmm) REVERT: A 551 ASN cc_start: 0.5365 (m-40) cc_final: 0.4932 (m-40) REVERT: A 619 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: A 634 HIS cc_start: 0.6645 (t70) cc_final: 0.6180 (t-90) REVERT: A 635 ARG cc_start: 0.8182 (mmt180) cc_final: 0.6927 (tpt170) REVERT: A 811 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 812 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.5781 (ttm-80) outliers start: 31 outliers final: 19 residues processed: 122 average time/residue: 0.0732 time to fit residues: 11.9894 Evaluate side-chains 116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 119 LEU 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 346 ILE 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 619 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.207408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.168538 restraints weight = 8733.618| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.45 r_work: 0.4037 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6747 Z= 0.131 Angle : 0.576 6.799 9218 Z= 0.304 Chirality : 0.045 0.132 1041 Planarity : 0.005 0.076 1116 Dihedral : 15.197 120.378 1157 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.73 % Allowed : 14.33 % Favored : 80.95 % 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: 234 sheet: -1.38 (0.38), residues: 179 loop : -0.95 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.014 0.001 TYR A 101 PHE 0.023 0.002 PHE A 746 TRP 0.010 0.001 TRP A 451 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6747) covalent geometry : angle 0.57561 / 0.30 ( 9218) hydrogen bonds : bond 0.03926 / 3.43 ( 242) hydrogen bonds : angle 5.52356 / 4.73 ( 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: 32 poor density : 99 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7151 (ttp) cc_final: 0.6684 (ttt) REVERT: A 48 ASP cc_start: 0.6215 (t0) cc_final: 0.5700 (p0) REVERT: A 82 PHE cc_start: 0.4559 (m-80) cc_final: 0.4340 (m-80) REVERT: A 166 MET cc_start: 0.7154 (mmp) cc_final: 0.6592 (mmt) REVERT: A 169 LEU cc_start: 0.4715 (OUTLIER) cc_final: 0.4427 (tp) REVERT: A 186 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4283 (pm20) REVERT: A 212 LYS cc_start: 0.8270 (pttm) cc_final: 0.7642 (ptmt) REVERT: A 225 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.4580 (m-80) REVERT: A 346 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5992 (mp) REVERT: A 402 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7650 (mmmm) REVERT: A 446 ILE cc_start: 0.7468 (mp) cc_final: 0.7130 (tt) REVERT: A 551 ASN cc_start: 0.5432 (m-40) cc_final: 0.5070 (m-40) REVERT: A 619 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: A 634 HIS cc_start: 0.6737 (t70) cc_final: 0.6260 (t-90) REVERT: A 635 ARG cc_start: 0.8227 (mmt180) cc_final: 0.6982 (tpt170) REVERT: A 811 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: A 812 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.5787 (ttm-80) outliers start: 32 outliers final: 24 residues processed: 119 average time/residue: 0.0839 time to fit residues: 13.1062 Evaluate side-chains 120 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 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 559 THR 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 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: 0.0060 chunk 7 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.3132 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.210196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.171615 restraints weight = 8663.009| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.45 r_work: 0.4075 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6747 Z= 0.108 Angle : 0.557 7.353 9218 Z= 0.293 Chirality : 0.044 0.132 1041 Planarity : 0.005 0.071 1116 Dihedral : 15.110 118.188 1157 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.55 % Allowed : 15.95 % Favored : 80.50 % 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: -1.10 (0.31), residues: 758 helix: 0.21 (0.35), residues: 234 sheet: -1.44 (0.37), residues: 184 loop : -0.83 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 506 TYR 0.012 0.001 TYR A 101 PHE 0.017 0.001 PHE A 746 TRP 0.009 0.001 TRP A 451 HIS 0.005 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 6747) covalent geometry : angle 0.55727 / 0.29 ( 9218) hydrogen bonds : bond 0.03618 / 3.12 ( 242) hydrogen bonds : angle 5.29142 / 4.62 ( 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 117 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.223 Fit side-chains REVERT: A 48 ASP cc_start: 0.6215 (t0) cc_final: 0.5958 (m-30) REVERT: A 82 PHE cc_start: 0.4660 (m-80) cc_final: 0.4459 (m-80) REVERT: A 186 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4145 (pm20) REVERT: A 225 TYR cc_start: 0.5517 (OUTLIER) cc_final: 0.4508 (m-80) REVERT: A 346 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5933 (mp) REVERT: A 400 MET cc_start: 0.6739 (mmm) cc_final: 0.5633 (ptp) REVERT: A 402 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7607 (mmmm) REVERT: A 446 ILE cc_start: 0.7475 (mp) cc_final: 0.7165 (tt) REVERT: A 619 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: A 634 HIS cc_start: 0.6664 (t70) cc_final: 0.6182 (t-90) REVERT: A 635 ARG cc_start: 0.8126 (mmt180) cc_final: 0.6883 (tpt170) REVERT: A 811 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: A 812 ARG cc_start: 0.7081 (mmm-85) cc_final: 0.5772 (ttm-80) outliers start: 24 outliers final: 15 residues processed: 109 average time/residue: 0.0779 time to fit residues: 11.3237 Evaluate side-chains 107 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 466 HIS 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 619 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 788 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.163343 restraints weight = 8639.634| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.39 r_work: 0.3936 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 6747 Z= 0.294 Angle : 0.758 11.769 9218 Z= 0.399 Chirality : 0.050 0.207 1041 Planarity : 0.006 0.087 1116 Dihedral : 15.326 116.899 1156 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.87 % Allowed : 15.95 % Favored : 79.17 % 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: -1.83 (0.30), residues: 758 helix: -0.64 (0.32), residues: 235 sheet: -1.81 (0.38), residues: 175 loop : -1.13 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 812 TYR 0.017 0.002 TYR A 529 PHE 0.030 0.003 PHE A 666 TRP 0.020 0.002 TRP A 451 HIS 0.013 0.002 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 ( 6747) covalent geometry : angle 0.75820 / 0.40 ( 9218) hydrogen bonds : bond 0.04926 / 4.38 ( 242) hydrogen bonds : angle 5.98129 / 5.10 ( 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 120 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6190 (t0) cc_final: 0.5976 (m-30) REVERT: A 82 PHE cc_start: 0.4688 (m-80) cc_final: 0.4452 (m-80) REVERT: A 169 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.4383 (tp) REVERT: A 186 GLU cc_start: 0.4440 (OUTLIER) cc_final: 0.3893 (pm20) REVERT: A 214 MET cc_start: 0.7978 (mtt) cc_final: 0.7726 (mtt) REVERT: A 346 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.5927 (mp) REVERT: A 400 MET cc_start: 0.6787 (mmm) cc_final: 0.5753 (ptp) REVERT: A 402 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7665 (mmmm) REVERT: A 619 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: A 635 ARG cc_start: 0.8326 (mmt180) cc_final: 0.7144 (tpt170) REVERT: A 811 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: A 812 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.5854 (ttm-80) outliers start: 33 outliers final: 23 residues processed: 111 average time/residue: 0.0866 time to fit residues: 12.7704 Evaluate side-chains 110 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 551 ASN A 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.206120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.170249 restraints weight = 8675.461| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.41 r_work: 0.4033 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6747 Z= 0.129 Angle : 0.621 9.068 9218 Z= 0.326 Chirality : 0.045 0.172 1041 Planarity : 0.005 0.086 1116 Dihedral : 15.208 114.835 1156 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.69 % Allowed : 17.28 % Favored : 79.03 % 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: -1.41 (0.31), residues: 758 helix: -0.15 (0.34), residues: 238 sheet: -1.66 (0.38), residues: 175 loop : -0.95 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.013 0.001 TYR A 101 PHE 0.015 0.002 PHE A 659 TRP 0.013 0.001 TRP A 451 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6747) covalent geometry : angle 0.62143 / 0.33 ( 9218) hydrogen bonds : bond 0.04028 / 3.45 ( 242) hydrogen bonds : angle 5.63442 / 4.86 ( 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 110 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6133 (t0) cc_final: 0.5848 (m-30) REVERT: A 82 PHE cc_start: 0.4761 (m-80) cc_final: 0.4519 (m-80) REVERT: A 186 GLU cc_start: 0.4802 (OUTLIER) cc_final: 0.4159 (pm20) REVERT: A 346 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5836 (mp) REVERT: A 400 MET cc_start: 0.6752 (mmm) cc_final: 0.5908 (ptp) REVERT: A 402 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7613 (mmmm) REVERT: A 483 MET cc_start: 0.7773 (ppp) cc_final: 0.7552 (ppp) REVERT: A 619 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: A 635 ARG cc_start: 0.8117 (mmt180) cc_final: 0.7044 (tpt170) REVERT: A 811 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: A 812 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.5731 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 0.0824 time to fit residues: 11.2386 Evaluate side-chains 102 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 619 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.206153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.170277 restraints weight = 8652.762| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.42 r_work: 0.4012 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6747 Z= 0.129 Angle : 0.602 9.796 9218 Z= 0.313 Chirality : 0.045 0.193 1041 Planarity : 0.005 0.073 1116 Dihedral : 15.044 112.362 1156 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.14 % Allowed : 17.13 % 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: -1.34 (0.31), residues: 758 helix: -0.14 (0.34), residues: 237 sheet: -1.57 (0.38), residues: 178 loop : -0.89 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.014 0.001 TYR A 101 PHE 0.011 0.001 PHE A 666 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 0.00299 / 0.13 ( 6747) covalent geometry : angle 0.60159 / 0.31 ( 9218) hydrogen bonds : bond 0.03773 / 3.27 ( 242) hydrogen bonds : angle 5.47931 / 4.79 ( 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 115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.6066 (t0) cc_final: 0.5702 (m-30) REVERT: A 82 PHE cc_start: 0.4765 (m-80) cc_final: 0.4520 (m-80) REVERT: A 129 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7096 (mtpp) REVERT: A 186 GLU cc_start: 0.4813 (OUTLIER) cc_final: 0.4212 (pm20) REVERT: A 346 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5828 (mp) REVERT: A 400 MET cc_start: 0.6854 (mmm) cc_final: 0.5946 (ptp) REVERT: A 402 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7616 (mmmm) REVERT: A 437 MET cc_start: 0.5687 (mtp) cc_final: 0.5382 (tpp) REVERT: A 619 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: A 635 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7081 (tpt170) REVERT: A 811 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: A 812 ARG cc_start: 0.6998 (mmm-85) cc_final: 0.6748 (mmm-85) outliers start: 28 outliers final: 21 residues processed: 107 average time/residue: 0.0811 time to fit residues: 11.5291 Evaluate side-chains 112 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 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 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 623 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.206424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167821 restraints weight = 8616.252| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.43 r_work: 0.4042 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2572 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= 0.129 Angle : 0.605 10.123 9218 Z= 0.315 Chirality : 0.045 0.168 1041 Planarity : 0.005 0.082 1116 Dihedral : 14.997 109.906 1156 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.84 % Allowed : 17.28 % Favored : 78.88 % 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: -1.30 (0.31), residues: 758 helix: -0.11 (0.34), residues: 237 sheet: -1.59 (0.37), residues: 184 loop : -0.81 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.024 0.001 TYR A 101 PHE 0.018 0.002 PHE A 659 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 0.00293 / 0.13 ( 6747) covalent geometry : angle 0.60463 / 0.31 ( 9218) hydrogen bonds : bond 0.03752 / 3.27 ( 242) hydrogen bonds : angle 5.37137 / 4.72 ( 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 114 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5428 (ttt) cc_final: 0.5159 (ttt) REVERT: A 48 ASP cc_start: 0.5988 (t0) cc_final: 0.5733 (m-30) REVERT: A 82 PHE cc_start: 0.4864 (m-80) cc_final: 0.4595 (m-80) REVERT: A 129 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7126 (mtpp) REVERT: A 186 GLU cc_start: 0.4782 (OUTLIER) cc_final: 0.4202 (pm20) REVERT: A 346 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5834 (mp) REVERT: A 400 MET cc_start: 0.6878 (mmm) cc_final: 0.6134 (mtm) REVERT: A 402 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7482 (mmmm) REVERT: A 437 MET cc_start: 0.5840 (mtp) cc_final: 0.5635 (mmm) REVERT: A 619 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: A 635 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7013 (tpt170) REVERT: A 778 GLU cc_start: 0.7873 (tp30) cc_final: 0.7576 (tp30) REVERT: A 811 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: A 812 ARG cc_start: 0.6942 (mmm-85) cc_final: 0.6683 (mmm-85) outliers start: 26 outliers final: 20 residues processed: 106 average time/residue: 0.0854 time to fit residues: 11.9447 Evaluate side-chains 109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 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 576 ASN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 619 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.0070 chunk 56 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.207487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.172307 restraints weight = 8615.060| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.42 r_work: 0.4052 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6747 Z= 0.119 Angle : 0.589 10.192 9218 Z= 0.305 Chirality : 0.045 0.167 1041 Planarity : 0.005 0.074 1116 Dihedral : 14.881 107.015 1156 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.99 % Allowed : 17.28 % 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: -1.27 (0.31), residues: 758 helix: -0.04 (0.34), residues: 241 sheet: -1.56 (0.37), residues: 184 loop : -0.84 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 506 TYR 0.017 0.001 TYR A 101 PHE 0.015 0.001 PHE A 659 TRP 0.009 0.001 TRP A 435 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6747) covalent geometry : angle 0.58948 / 0.31 ( 9218) hydrogen bonds : bond 0.03599 / 3.11 ( 242) hydrogen bonds : angle 5.18528 / 4.63 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.02 seconds wall clock time: 28 minutes 12.70 seconds (1692.70 seconds total)