Starting phenix.real_space_refine on Sun Aug 24 02:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056.map" model { file = "/net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q0n_18056/08_2025/8q0n_18056_trim.cif" } resolution = 4.2 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= 0.009 sd= 0.124 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 56 5.16 5 C 5080 2.51 5 N 1360 2.21 5 O 1508 1.98 5 H 7910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15917 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 13084 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 39, 'TRANS': 791} Chain breaks: 2 Chain: "C" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2798 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 11, 'TRANS': 166} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'04E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'04E:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.17 Number of scatterers: 15917 At special positions: 0 Unit cell: (80.898, 92.574, 146.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 O 1508 8.00 N 1360 7.00 C 5080 6.00 H 7910 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 382.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 65.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 26 through 41 Proline residue: B 36 - end of helix removed outlier: 4.193A pdb=" N MET B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.594A pdb=" N SER B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.776A pdb=" N LEU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.578A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.875A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.965A pdb=" N VAL B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 231 through 240 removed outlier: 4.032A pdb=" N LEU B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.511A pdb=" N CYS B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.265A pdb=" N GLN B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.720A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 312 through 333 removed outlier: 3.556A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.587A pdb=" N VAL B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 395 removed outlier: 3.655A pdb=" N LEU B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 465 removed outlier: 3.542A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 3.616A pdb=" N PHE B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 495 through 501 removed outlier: 4.323A pdb=" N PHE B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.650A pdb=" N LEU B 506 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.875A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 522 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 538 removed outlier: 3.720A pdb=" N TRP B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 534 " --> pdb=" O TRP B 530 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 Processing helix chain 'B' and resid 574 through 580 Processing helix chain 'B' and resid 593 through 610 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.537A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 655 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 676 through 683 Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 726 through 730 Processing helix chain 'B' and resid 736 through 750 removed outlier: 3.843A pdb=" N GLU B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 765 Processing helix chain 'B' and resid 769 through 775 removed outlier: 3.668A pdb=" N LEU B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 787 Processing helix chain 'B' and resid 793 through 798 Processing helix chain 'B' and resid 809 through 823 Processing helix chain 'B' and resid 824 through 837 removed outlier: 3.525A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.873A pdb=" N ALA B 847 " --> pdb=" O GLY B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.790A pdb=" N ARG C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.511A pdb=" N PHE C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.790A pdb=" N ILE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.607A pdb=" N GLY C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 178 removed outlier: 3.767A pdb=" N VAL C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.664A pdb=" N PHE B 61 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 66 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 555 through 557 removed outlier: 5.298A pdb=" N LEU B 555 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 616 through 618 Processing sheet with id=AA4, first strand: chain 'B' and resid 709 through 714 removed outlier: 3.596A pdb=" N VAL B 710 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 721 " --> pdb=" O VAL B 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 850 through 851 removed outlier: 3.529A pdb=" N GLY B 854 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 859 through 863 Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 46 removed outlier: 4.044A pdb=" N ASP C 38 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 57 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 2 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL C 77 " --> pdb=" O ALA C 3 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS C 5 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU C 79 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 7 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N CYS C 81 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 9 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N SER C 83 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE C 78 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 113 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 80 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR C 115 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE C 82 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 153 " --> pdb=" O ILE C 110 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7882 1.03 - 1.23: 119 1.23 - 1.43: 3302 1.43 - 1.62: 4706 1.62 - 1.82: 83 Bond restraints: 16092 Sorted by residual: bond pdb=" N GLU B 22 " pdb=" CA GLU B 22 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 22 " pdb=" H GLU B 22 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N MET C 1 " pdb=" H MET C 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 04E B1001 " pdb=" O1 04E B1001 " ideal model delta sigma weight residual 1.235 1.259 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 16087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 28447 1.41 - 2.81: 599 2.81 - 4.22: 43 4.22 - 5.63: 11 5.63 - 7.03: 1 Bond angle restraints: 29101 Sorted by residual: angle pdb=" C2' GTP C 201 " pdb=" C3' GTP C 201 " pdb=" C4' GTP C 201 " ideal model delta sigma weight residual 111.00 103.97 7.03 3.00e+00 1.11e-01 5.50e+00 angle pdb=" CA GLN B 774 " pdb=" CB GLN B 774 " pdb=" CG GLN B 774 " ideal model delta sigma weight residual 114.10 118.70 -4.60 2.00e+00 2.50e-01 5.29e+00 angle pdb=" CA MET B 37 " pdb=" CB MET B 37 " pdb=" CG MET B 37 " ideal model delta sigma weight residual 114.10 118.56 -4.46 2.00e+00 2.50e-01 4.96e+00 angle pdb=" N TYR C 72 " pdb=" CA TYR C 72 " pdb=" C TYR C 72 " ideal model delta sigma weight residual 109.81 114.45 -4.64 2.21e+00 2.05e-01 4.41e+00 angle pdb=" C ARG B 655 " pdb=" CA ARG B 655 " pdb=" CB ARG B 655 " ideal model delta sigma weight residual 111.06 107.66 3.40 1.83e+00 2.99e-01 3.45e+00 ... (remaining 29096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 7355 29.79 - 59.59: 227 59.59 - 89.38: 13 89.38 - 119.18: 0 119.18 - 148.97: 2 Dihedral angle restraints: 7597 sinusoidal: 4152 harmonic: 3445 Sorted by residual: dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 -141.76 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -23.95 128.54 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CG LYS B 488 " pdb=" CD LYS B 488 " pdb=" CE LYS B 488 " pdb=" NZ LYS B 488 " ideal model delta sinusoidal sigma weight residual 180.00 121.70 58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 838 0.027 - 0.054: 261 0.054 - 0.081: 92 0.081 - 0.108: 43 0.108 - 0.135: 23 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PRO B 200 " pdb=" N PRO B 200 " pdb=" C PRO B 200 " pdb=" CB PRO B 200 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE B 860 " pdb=" N ILE B 860 " pdb=" C ILE B 860 " pdb=" CB ILE B 860 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1254 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 68 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 69 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 788 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 789 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 789 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 789 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 33 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 34 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.020 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 943 2.20 - 2.80: 32970 2.80 - 3.40: 43521 3.40 - 4.00: 54471 4.00 - 4.60: 83996 Nonbonded interactions: 215901 Sorted by model distance: nonbonded pdb=" OE1 GLU B 285 " pdb=" H GLU B 285 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP C 11 " pdb=" HE1 TRP C 97 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASP C 65 " pdb="HH22 ARG C 68 " model vdw 1.667 2.450 nonbonded pdb=" OE1 GLN B 756 " pdb=" H GLN B 756 " model vdw 1.677 2.450 nonbonded pdb=" H THR B 733 " pdb=" OD1 ASN B 736 " model vdw 1.680 2.450 ... (remaining 215896 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 group one per residue 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: 1.990 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4431 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 : 0.003 0.199 8184 Z= 0.240 Angle : 0.477 7.034 11113 Z= 0.239 Chirality : 0.036 0.135 1257 Planarity : 0.004 0.055 1431 Dihedral : 13.782 148.971 3024 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.27), residues: 1001 helix: 1.36 (0.22), residues: 544 sheet: 0.59 (0.76), residues: 50 loop : 0.34 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 120 TYR 0.013 0.001 TYR B 313 PHE 0.015 0.001 PHE C 37 TRP 0.008 0.001 TRP C 97 HIS 0.007 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8182) covalent geometry : angle 0.47664 (11113) hydrogen bonds : bond 0.25984 ( 419) hydrogen bonds : angle 7.62510 ( 1221) Misc. bond : bond 0.14136 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.4626 (p90) cc_final: 0.4300 (p90) REVERT: B 114 MET cc_start: 0.3889 (mmt) cc_final: 0.3679 (mmt) REVERT: B 312 ASN cc_start: 0.9012 (t0) cc_final: 0.8805 (t0) REVERT: B 634 ASN cc_start: 0.7705 (t0) cc_final: 0.7495 (t0) REVERT: B 718 MET cc_start: 0.5410 (tpp) cc_final: 0.5079 (tpp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1443 time to fit residues: 29.5654 Evaluate side-chains 128 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 173 GLN B 302 ASN B 697 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.181028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.153484 restraints weight = 36252.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.154306 restraints weight = 41780.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.151429 restraints weight = 22370.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.152557 restraints weight = 17391.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153037 restraints weight = 13539.230| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8184 Z= 0.219 Angle : 0.644 7.902 11113 Z= 0.348 Chirality : 0.041 0.156 1257 Planarity : 0.005 0.058 1431 Dihedral : 8.243 169.978 1094 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.11 % Allowed : 2.91 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1001 helix: 0.77 (0.20), residues: 586 sheet: -0.01 (0.76), residues: 44 loop : 0.15 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 120 TYR 0.016 0.002 TYR B 202 PHE 0.011 0.002 PHE C 90 TRP 0.009 0.001 TRP C 97 HIS 0.010 0.002 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8182) covalent geometry : angle 0.64396 (11113) hydrogen bonds : bond 0.05648 ( 419) hydrogen bonds : angle 5.81009 ( 1221) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8192 (t0) cc_final: 0.7705 (p0) REVERT: B 92 ASN cc_start: 0.7979 (t0) cc_final: 0.7753 (t0) REVERT: B 114 MET cc_start: 0.7405 (mmt) cc_final: 0.6911 (mmt) REVERT: B 163 MET cc_start: 0.4823 (ptm) cc_final: 0.4542 (ptm) REVERT: B 209 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8329 (mm-40) REVERT: B 646 GLN cc_start: 0.7079 (mt0) cc_final: 0.6727 (mt0) REVERT: B 718 MET cc_start: 0.5320 (tpp) cc_final: 0.4780 (tpp) REVERT: B 742 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 743 LEU cc_start: 0.9174 (mm) cc_final: 0.8814 (mm) REVERT: B 846 PHE cc_start: 0.6493 (m-80) cc_final: 0.6037 (m-80) REVERT: C 55 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6072 (mp) REVERT: C 75 THR cc_start: 0.7552 (m) cc_final: 0.7045 (m) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1399 time to fit residues: 26.9285 Evaluate side-chains 113 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS B 355 GLN B 594 GLN B 656 GLN C 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.178753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147084 restraints weight = 36937.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153309 restraints weight = 34253.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153562 restraints weight = 16801.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154222 restraints weight = 12659.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155018 restraints weight = 11488.652| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8184 Z= 0.159 Angle : 0.551 6.947 11113 Z= 0.295 Chirality : 0.039 0.159 1257 Planarity : 0.005 0.091 1431 Dihedral : 8.293 177.937 1094 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.11 % Allowed : 1.57 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 1001 helix: 0.73 (0.21), residues: 588 sheet: -0.53 (0.74), residues: 48 loop : 0.16 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.011 0.001 TYR B 202 PHE 0.015 0.001 PHE B 459 TRP 0.006 0.001 TRP C 97 HIS 0.006 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8182) covalent geometry : angle 0.55053 (11113) hydrogen bonds : bond 0.05265 ( 419) hydrogen bonds : angle 5.45688 ( 1221) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8149 (t0) cc_final: 0.7713 (p0) REVERT: B 114 MET cc_start: 0.7275 (mmt) cc_final: 0.7005 (mmt) REVERT: B 209 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8064 (mm-40) REVERT: B 646 GLN cc_start: 0.6697 (mt0) cc_final: 0.6183 (mt0) REVERT: B 718 MET cc_start: 0.5214 (tpp) cc_final: 0.4733 (tpp) REVERT: B 742 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 743 LEU cc_start: 0.8927 (mm) cc_final: 0.8506 (mm) REVERT: C 75 THR cc_start: 0.7418 (m) cc_final: 0.6840 (m) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1435 time to fit residues: 27.4519 Evaluate side-chains 102 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 2 optimal weight: 0.0070 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.181427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148803 restraints weight = 36578.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149635 restraints weight = 29923.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.151997 restraints weight = 22532.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.152524 restraints weight = 13513.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155385 restraints weight = 12688.860| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8184 Z= 0.115 Angle : 0.510 6.769 11113 Z= 0.268 Chirality : 0.038 0.139 1257 Planarity : 0.004 0.051 1431 Dihedral : 8.060 175.885 1094 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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 aren not related in a simple way. whole: 0.71 (0.27), residues: 1001 helix: 0.80 (0.21), residues: 590 sheet: -0.29 (0.77), residues: 47 loop : 0.26 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 527 TYR 0.009 0.001 TYR B 313 PHE 0.015 0.001 PHE B 459 TRP 0.039 0.002 TRP B 364 HIS 0.004 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8182) covalent geometry : angle 0.51010 (11113) hydrogen bonds : bond 0.04354 ( 419) hydrogen bonds : angle 5.23384 ( 1221) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8129 (t0) cc_final: 0.7677 (p0) REVERT: B 209 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7909 (mm-40) REVERT: B 278 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6790 (mt-10) REVERT: B 646 GLN cc_start: 0.6891 (mt0) cc_final: 0.6321 (mt0) REVERT: B 718 MET cc_start: 0.5340 (tpp) cc_final: 0.4809 (tpp) REVERT: C 75 THR cc_start: 0.7036 (m) cc_final: 0.6666 (m) REVERT: C 119 LEU cc_start: 0.7820 (mm) cc_final: 0.7439 (mt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1342 time to fit residues: 25.2692 Evaluate side-chains 112 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.179831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148168 restraints weight = 36655.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147707 restraints weight = 30899.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150366 restraints weight = 26155.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.151082 restraints weight = 14893.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.153859 restraints weight = 13546.601| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8184 Z= 0.149 Angle : 0.538 7.103 11113 Z= 0.285 Chirality : 0.038 0.150 1257 Planarity : 0.004 0.051 1431 Dihedral : 8.150 175.177 1094 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.27), residues: 1001 helix: 0.75 (0.21), residues: 593 sheet: -0.87 (0.77), residues: 48 loop : 0.28 (0.36), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 120 TYR 0.021 0.002 TYR B 241 PHE 0.015 0.001 PHE B 256 TRP 0.019 0.001 TRP B 364 HIS 0.006 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8182) covalent geometry : angle 0.53823 (11113) hydrogen bonds : bond 0.04254 ( 419) hydrogen bonds : angle 5.22159 ( 1221) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8297 (t0) cc_final: 0.7780 (p0) REVERT: B 114 MET cc_start: 0.7493 (mmt) cc_final: 0.7262 (mmt) REVERT: B 163 MET cc_start: 0.5327 (ptm) cc_final: 0.4945 (ptm) REVERT: B 209 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7918 (mm-40) REVERT: B 278 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 646 GLN cc_start: 0.6703 (mt0) cc_final: 0.6183 (mt0) REVERT: B 718 MET cc_start: 0.5327 (tpp) cc_final: 0.4793 (tpp) REVERT: B 767 PHE cc_start: 0.8291 (m-80) cc_final: 0.7903 (m-10) REVERT: C 75 THR cc_start: 0.7367 (m) cc_final: 0.6779 (m) REVERT: C 119 LEU cc_start: 0.7571 (mm) cc_final: 0.7316 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1425 time to fit residues: 27.2622 Evaluate side-chains 111 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.0370 chunk 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.175304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.139076 restraints weight = 37323.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139276 restraints weight = 23590.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.141774 restraints weight = 18464.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142398 restraints weight = 12373.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145826 restraints weight = 11482.277| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8184 Z= 0.108 Angle : 0.503 6.686 11113 Z= 0.264 Chirality : 0.037 0.135 1257 Planarity : 0.004 0.048 1431 Dihedral : 7.893 171.082 1094 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.27), residues: 1001 helix: 1.04 (0.21), residues: 585 sheet: -0.83 (0.75), residues: 48 loop : 0.29 (0.36), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 353 TYR 0.009 0.001 TYR B 313 PHE 0.017 0.001 PHE B 502 TRP 0.008 0.001 TRP B 364 HIS 0.005 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8182) covalent geometry : angle 0.50257 (11113) hydrogen bonds : bond 0.03954 ( 419) hydrogen bonds : angle 5.02218 ( 1221) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8339 (t0) cc_final: 0.7693 (p0) REVERT: B 159 VAL cc_start: 0.8718 (m) cc_final: 0.8456 (p) REVERT: B 163 MET cc_start: 0.5514 (ptm) cc_final: 0.5154 (ptm) REVERT: B 209 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7790 (mm-40) REVERT: B 630 ASN cc_start: 0.8195 (t0) cc_final: 0.7870 (m110) REVERT: B 646 GLN cc_start: 0.6802 (mt0) cc_final: 0.6275 (mt0) REVERT: B 718 MET cc_start: 0.5372 (tpp) cc_final: 0.4828 (tpp) REVERT: B 767 PHE cc_start: 0.8314 (m-80) cc_final: 0.7784 (m-10) REVERT: C 75 THR cc_start: 0.7229 (m) cc_final: 0.6636 (m) REVERT: C 119 LEU cc_start: 0.7815 (mm) cc_final: 0.7548 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1674 time to fit residues: 30.5093 Evaluate side-chains 105 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.177225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146075 restraints weight = 36982.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143514 restraints weight = 31280.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146462 restraints weight = 29201.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.147483 restraints weight = 17368.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147727 restraints weight = 14883.411| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8184 Z= 0.174 Angle : 0.570 7.465 11113 Z= 0.305 Chirality : 0.039 0.150 1257 Planarity : 0.005 0.053 1431 Dihedral : 8.216 168.203 1094 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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 aren not related in a simple way. whole: 0.47 (0.27), residues: 1001 helix: 0.79 (0.21), residues: 581 sheet: -1.73 (0.70), residues: 48 loop : 0.05 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 107 TYR 0.014 0.002 TYR B 288 PHE 0.020 0.002 PHE B 479 TRP 0.008 0.001 TRP C 56 HIS 0.008 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8182) covalent geometry : angle 0.57016 (11113) hydrogen bonds : bond 0.04294 ( 419) hydrogen bonds : angle 5.31962 ( 1221) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8471 (t0) cc_final: 0.7790 (p0) REVERT: B 92 ASN cc_start: 0.7988 (t0) cc_final: 0.7761 (t0) REVERT: B 114 MET cc_start: 0.7500 (mmt) cc_final: 0.7261 (mmt) REVERT: B 159 VAL cc_start: 0.8670 (m) cc_final: 0.8457 (p) REVERT: B 163 MET cc_start: 0.5824 (ptm) cc_final: 0.5523 (ptm) REVERT: B 209 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7937 (mm-40) REVERT: B 630 ASN cc_start: 0.8000 (t0) cc_final: 0.7799 (m110) REVERT: B 646 GLN cc_start: 0.6809 (mt0) cc_final: 0.6412 (mt0) REVERT: B 718 MET cc_start: 0.5385 (tpp) cc_final: 0.4829 (tpp) REVERT: B 742 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 743 LEU cc_start: 0.9053 (mm) cc_final: 0.8601 (mm) REVERT: B 767 PHE cc_start: 0.8359 (m-80) cc_final: 0.7957 (m-10) REVERT: B 774 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7283 (tm-30) REVERT: C 119 LEU cc_start: 0.7643 (mm) cc_final: 0.7357 (mt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1619 time to fit residues: 28.0529 Evaluate side-chains 108 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 56 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.179919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.147426 restraints weight = 36628.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146902 restraints weight = 32688.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149041 restraints weight = 24385.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.150390 restraints weight = 15566.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.150576 restraints weight = 14115.291| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8184 Z= 0.105 Angle : 0.496 6.456 11113 Z= 0.259 Chirality : 0.037 0.134 1257 Planarity : 0.004 0.052 1431 Dihedral : 7.743 161.341 1094 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.27), residues: 1001 helix: 1.09 (0.21), residues: 578 sheet: -1.39 (0.76), residues: 47 loop : 0.22 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.014 0.001 TYR B 288 PHE 0.012 0.001 PHE B 479 TRP 0.004 0.001 TRP B 693 HIS 0.005 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8182) covalent geometry : angle 0.49626 (11113) hydrogen bonds : bond 0.03819 ( 419) hydrogen bonds : angle 4.96978 ( 1221) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8358 (t0) cc_final: 0.7688 (p0) REVERT: B 92 ASN cc_start: 0.7966 (t0) cc_final: 0.7720 (t0) REVERT: B 159 VAL cc_start: 0.8684 (m) cc_final: 0.8437 (p) REVERT: B 163 MET cc_start: 0.5848 (ptm) cc_final: 0.5638 (ptm) REVERT: B 209 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7804 (mm-40) REVERT: B 467 MET cc_start: 0.4640 (ptt) cc_final: 0.4423 (ptt) REVERT: B 646 GLN cc_start: 0.6754 (mt0) cc_final: 0.6357 (mt0) REVERT: B 718 MET cc_start: 0.5414 (tpp) cc_final: 0.4854 (tpp) REVERT: B 742 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 743 LEU cc_start: 0.9065 (mm) cc_final: 0.8616 (mm) REVERT: B 767 PHE cc_start: 0.8315 (m-80) cc_final: 0.7961 (m-10) REVERT: B 774 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7241 (tm-30) REVERT: C 119 LEU cc_start: 0.7693 (mm) cc_final: 0.7394 (mt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1539 time to fit residues: 26.9108 Evaluate side-chains 104 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.178173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145738 restraints weight = 36638.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148792 restraints weight = 36435.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150758 restraints weight = 25540.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151050 restraints weight = 14800.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.151986 restraints weight = 13561.979| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8184 Z= 0.138 Angle : 0.530 6.837 11113 Z= 0.279 Chirality : 0.038 0.141 1257 Planarity : 0.004 0.052 1431 Dihedral : 7.829 160.806 1094 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.27), residues: 1001 helix: 1.01 (0.21), residues: 578 sheet: -1.67 (0.74), residues: 48 loop : 0.13 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.010 0.001 TYR B 288 PHE 0.008 0.001 PHE B 459 TRP 0.010 0.001 TRP B 796 HIS 0.005 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8182) covalent geometry : angle 0.53037 (11113) hydrogen bonds : bond 0.03938 ( 419) hydrogen bonds : angle 5.04849 ( 1221) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8422 (t0) cc_final: 0.7790 (p0) REVERT: B 92 ASN cc_start: 0.7980 (t0) cc_final: 0.7744 (t0) REVERT: B 159 VAL cc_start: 0.8689 (m) cc_final: 0.8437 (p) REVERT: B 209 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7844 (mm-40) REVERT: B 646 GLN cc_start: 0.6823 (mt0) cc_final: 0.6442 (mt0) REVERT: B 718 MET cc_start: 0.5422 (tpp) cc_final: 0.4839 (tpp) REVERT: B 742 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 743 LEU cc_start: 0.9047 (mm) cc_final: 0.8563 (mm) REVERT: B 767 PHE cc_start: 0.8345 (m-80) cc_final: 0.8040 (m-10) REVERT: B 774 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 119 LEU cc_start: 0.7686 (mm) cc_final: 0.7412 (mt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1673 time to fit residues: 28.9919 Evaluate side-chains 112 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 88 optimal weight: 0.4980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.179872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146692 restraints weight = 37033.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145909 restraints weight = 28575.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.148849 restraints weight = 21867.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149633 restraints weight = 13135.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.150200 restraints weight = 12583.112| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8184 Z= 0.102 Angle : 0.496 6.382 11113 Z= 0.257 Chirality : 0.037 0.140 1257 Planarity : 0.004 0.050 1431 Dihedral : 7.583 156.444 1094 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 1001 helix: 1.17 (0.21), residues: 579 sheet: -1.46 (0.74), residues: 48 loop : 0.16 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.007 0.001 TYR B 288 PHE 0.015 0.001 PHE B 531 TRP 0.006 0.001 TRP B 796 HIS 0.004 0.001 HIS B 503 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8182) covalent geometry : angle 0.49560 (11113) hydrogen bonds : bond 0.03665 ( 419) hydrogen bonds : angle 4.88091 ( 1221) Misc. bond : bond 0.00004 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 147 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASN cc_start: 0.8462 (t0) cc_final: 0.7774 (p0) REVERT: B 92 ASN cc_start: 0.8002 (t0) cc_final: 0.7741 (t0) REVERT: B 159 VAL cc_start: 0.8771 (m) cc_final: 0.8515 (p) REVERT: B 209 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7770 (mm-40) REVERT: B 646 GLN cc_start: 0.6863 (mt0) cc_final: 0.6508 (mt0) REVERT: B 718 MET cc_start: 0.5436 (tpp) cc_final: 0.4851 (tpp) REVERT: B 742 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 743 LEU cc_start: 0.9110 (mm) cc_final: 0.8656 (mm) REVERT: B 767 PHE cc_start: 0.8348 (m-80) cc_final: 0.8020 (m-10) REVERT: B 774 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 119 LEU cc_start: 0.7750 (mm) cc_final: 0.7463 (mt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1569 time to fit residues: 26.0047 Evaluate side-chains 105 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.178594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146385 restraints weight = 36336.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148820 restraints weight = 33194.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151114 restraints weight = 23275.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.150678 restraints weight = 14821.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.151583 restraints weight = 13389.418| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8184 Z= 0.122 Angle : 0.513 6.717 11113 Z= 0.267 Chirality : 0.038 0.139 1257 Planarity : 0.004 0.051 1431 Dihedral : 7.600 154.783 1094 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1001 helix: 1.13 (0.21), residues: 579 sheet: -1.74 (0.74), residues: 48 loop : 0.14 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.009 0.001 TYR B 288 PHE 0.010 0.001 PHE B 256 TRP 0.005 0.001 TRP C 56 HIS 0.004 0.001 HIS B 279 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8182) covalent geometry : angle 0.51295 (11113) hydrogen bonds : bond 0.03696 ( 419) hydrogen bonds : angle 4.93131 ( 1221) Misc. bond : bond 0.00005 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.41 seconds wall clock time: 36 minutes 43.58 seconds (2203.58 seconds total)