Starting phenix.real_space_refine (version: dev) on Sun Dec 11 22:13:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a69_6987/12_2022/6a69_6987.pdb" } resolution = 4.11 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7851 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6839 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 36, 'TRANS': 847} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 1012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1009 Unusual residues: {'NAG': 1} Classifications: {'peptide': 127, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118, None: 1} Not linked: pdbres="LYS B 246 " pdbres="NAG B 301 " Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 128, 1009 Unusual residues: {'NAG': 1} Classifications: {'peptide': 127, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 118, None: 1} Not linked: pdbres="LYS B 246 " pdbres="NAG B 301 " Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1028 Time building chain proxies: 5.41, per 1000 atoms: 0.69 Number of scatterers: 7851 At special positions: 0 Unit cell: (134.193, 103.645, 128.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1443 8.00 N 1324 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG B 301 " - " ASN B 168 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 9 sheets defined 43.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 153 through 190 removed outlier: 3.994A pdb=" N ALA A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.815A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.969A pdb=" N VAL A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 461 through 466 removed outlier: 3.945A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.733A pdb=" N CYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 4.086A pdb=" N VAL A 563 " --> pdb=" O ASP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.842A pdb=" N LYS A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.973A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 757 Processing helix chain 'A' and resid 769 through 781 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.857A pdb=" N LEU A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 834 through 877 removed outlier: 3.726A pdb=" N ILE A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 849 " --> pdb=" O GLY A 845 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 903 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.672A pdb=" N LEU A 912 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 913 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 925 through 949 Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.667A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 4.004A pdb=" N LEU A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A1025 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1058 removed outlier: 3.913A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.533A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.982A pdb=" N ILE A 472 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 707 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER A 474 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 765 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET A 706 " --> pdb=" O LEU A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.866A pdb=" N GLU A 683 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 589 removed outlier: 3.650A pdb=" N MET A 585 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 613 through 616 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 126 removed outlier: 6.471A pdb=" N LYS B 144 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 143 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 6.202A pdb=" N GLU B 131 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 211 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 200 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 197 " --> pdb=" O LYS B 158 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1038 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: 2.42 Time building geometry restraints manager: 3.43 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: 2391 1.34 - 1.46: 1487 1.46 - 1.58: 4055 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 7994 Sorted by residual: bond pdb=" C TRP A 759 " pdb=" N PRO A 760 " ideal model delta sigma weight residual 1.331 1.364 -0.032 7.90e-03 1.60e+04 1.64e+01 bond pdb=" C ALA B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.333 1.363 -0.030 7.80e-03 1.64e+04 1.46e+01 bond pdb=" CG GLN A1020 " pdb=" CD GLN A1020 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.61e+00 bond pdb=" CB TRP A 759 " pdb=" CG TRP A 759 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.81e+00 bond pdb=" CB VAL A 792 " pdb=" CG2 VAL A 792 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 ... (remaining 7989 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.66: 165 104.66 - 112.73: 4306 112.73 - 120.80: 3934 120.80 - 128.87: 2380 128.87 - 136.94: 81 Bond angle restraints: 10866 Sorted by residual: angle pdb=" N HIS A 965 " pdb=" CA HIS A 965 " pdb=" C HIS A 965 " ideal model delta sigma weight residual 111.07 118.76 -7.69 1.07e+00 8.73e-01 5.17e+01 angle pdb=" N GLY A 228 " pdb=" CA GLY A 228 " pdb=" C GLY A 228 " ideal model delta sigma weight residual 111.42 121.78 -10.36 1.51e+00 4.39e-01 4.71e+01 angle pdb=" N PRO A 67 " pdb=" CA PRO A 67 " pdb=" CB PRO A 67 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 angle pdb=" C PRO A 530 " pdb=" N PRO A 531 " pdb=" CD PRO A 531 " ideal model delta sigma weight residual 120.60 107.98 12.62 2.20e+00 2.07e-01 3.29e+01 angle pdb=" C GLU A 689 " pdb=" N VAL A 690 " pdb=" CA VAL A 690 " ideal model delta sigma weight residual 120.43 125.52 -5.09 9.60e-01 1.09e+00 2.81e+01 ... (remaining 10861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 4378 15.21 - 30.42: 323 30.42 - 45.64: 72 45.64 - 60.85: 11 60.85 - 76.06: 4 Dihedral angle restraints: 4788 sinusoidal: 1807 harmonic: 2981 Sorted by residual: dihedral pdb=" CA VAL A 680 " pdb=" C VAL A 680 " pdb=" N GLY A 681 " pdb=" CA GLY A 681 " ideal model delta harmonic sigma weight residual 180.00 126.37 53.63 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N GLU A 566 " pdb=" CA GLU A 566 " ideal model delta harmonic sigma weight residual 0.00 44.37 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA PHE A 953 " pdb=" C PHE A 953 " pdb=" N PHE A 954 " pdb=" CA PHE A 954 " ideal model delta harmonic sigma weight residual -180.00 -137.23 -42.77 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1016 0.080 - 0.160: 259 0.160 - 0.240: 28 0.240 - 0.320: 4 0.320 - 0.400: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CB ILE A1061 " pdb=" CA ILE A1061 " pdb=" CG1 ILE A1061 " pdb=" CG2 ILE A1061 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA HIS A 965 " pdb=" N HIS A 965 " pdb=" C HIS A 965 " pdb=" CB HIS A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL A 680 " pdb=" CA VAL A 680 " pdb=" CG1 VAL A 680 " pdb=" CG2 VAL A 680 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1305 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 94 " -0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO A 95 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 638 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO A 639 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 639 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 639 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 225 " 0.015 2.00e-02 2.50e+03 1.81e-02 8.22e+00 pdb=" CG TRP B 225 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 225 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 225 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 225 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 225 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2026 2.80 - 3.32: 7367 3.32 - 3.85: 12435 3.85 - 4.37: 13360 4.37 - 4.90: 22735 Nonbonded interactions: 57923 Sorted by model distance: nonbonded pdb=" O VAL A 515 " pdb=" OG SER A 519 " model vdw 2.275 2.440 nonbonded pdb=" O TYR A 513 " pdb=" OG1 THR A 516 " model vdw 2.308 2.440 nonbonded pdb=" O LEU A 947 " pdb=" NH1 ARG A 960 " model vdw 2.344 2.520 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 125 " model vdw 2.345 2.440 nonbonded pdb=" OE2 GLU B 135 " pdb=" NE2 GLN B 190 " model vdw 2.350 2.520 ... (remaining 57918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5045 2.51 5 N 1324 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 0.530 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: 2.650 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 25.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.011 0.105 7994 Z= 0.687 Angle : 1.468 14.780 10866 Z= 0.799 Chirality : 0.069 0.400 1308 Planarity : 0.009 0.077 1372 Dihedral : 11.854 76.061 2857 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.53 % Favored : 86.37 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.43 % Twisted Proline : 0.00 % Twisted General : 0.91 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.21), residues: 1021 helix: -2.43 (0.19), residues: 449 sheet: -2.74 (0.46), residues: 103 loop : -3.93 (0.22), residues: 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 240 average time/residue: 0.1812 time to fit residues: 59.8021 Evaluate side-chains 139 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1539 time to fit residues: 2.5759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 540 HIS A 711 ASN A 886 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7994 Z= 0.198 Angle : 0.850 16.650 10866 Z= 0.408 Chirality : 0.045 0.193 1308 Planarity : 0.006 0.074 1372 Dihedral : 6.987 43.872 1096 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.92 % Favored : 90.88 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.24), residues: 1021 helix: -0.58 (0.23), residues: 462 sheet: -2.76 (0.43), residues: 107 loop : -3.61 (0.24), residues: 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.1527 time to fit residues: 48.2550 Evaluate side-chains 133 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0656 time to fit residues: 1.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 75 optimal weight: 0.9980 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7994 Z= 0.196 Angle : 0.823 16.127 10866 Z= 0.390 Chirality : 0.045 0.187 1308 Planarity : 0.006 0.084 1372 Dihedral : 6.480 42.817 1096 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.80 % Favored : 90.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.25), residues: 1021 helix: 0.22 (0.24), residues: 457 sheet: -2.54 (0.45), residues: 106 loop : -3.43 (0.25), residues: 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1643 time to fit residues: 44.2162 Evaluate side-chains 130 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 711 ASN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 7994 Z= 0.234 Angle : 0.800 16.618 10866 Z= 0.382 Chirality : 0.044 0.174 1308 Planarity : 0.005 0.076 1372 Dihedral : 6.107 43.447 1096 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.02 % Favored : 90.78 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.25), residues: 1021 helix: 0.48 (0.24), residues: 458 sheet: -2.25 (0.47), residues: 107 loop : -3.45 (0.25), residues: 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 178 average time/residue: 0.1552 time to fit residues: 40.1854 Evaluate side-chains 130 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0720 time to fit residues: 1.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7994 Z= 0.252 Angle : 0.802 16.060 10866 Z= 0.384 Chirality : 0.045 0.175 1308 Planarity : 0.005 0.078 1372 Dihedral : 5.996 43.314 1096 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.29 % Favored : 89.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.26), residues: 1021 helix: 0.63 (0.25), residues: 458 sheet: -2.24 (0.46), residues: 114 loop : -3.41 (0.25), residues: 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1561 time to fit residues: 39.9072 Evaluate side-chains 123 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN A 752 GLN A 859 GLN ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7994 Z= 0.178 Angle : 0.772 15.787 10866 Z= 0.365 Chirality : 0.044 0.181 1308 Planarity : 0.005 0.081 1372 Dihedral : 5.780 42.228 1096 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.55 % Favored : 92.25 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.26), residues: 1021 helix: 0.88 (0.25), residues: 456 sheet: -2.01 (0.47), residues: 114 loop : -3.28 (0.25), residues: 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.1476 time to fit residues: 38.4335 Evaluate side-chains 129 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0682 time to fit residues: 1.3554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 GLN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7994 Z= 0.198 Angle : 0.775 16.356 10866 Z= 0.368 Chirality : 0.044 0.177 1308 Planarity : 0.005 0.082 1372 Dihedral : 5.649 43.075 1096 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.31 % Favored : 90.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.26), residues: 1021 helix: 0.92 (0.25), residues: 462 sheet: -1.91 (0.48), residues: 114 loop : -3.17 (0.26), residues: 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1543 time to fit residues: 38.5031 Evaluate side-chains 131 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.0050 chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0470 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 overall best weight: 0.7494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN A 711 ASN ** A 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7994 Z= 0.181 Angle : 0.764 15.486 10866 Z= 0.360 Chirality : 0.043 0.179 1308 Planarity : 0.005 0.083 1372 Dihedral : 5.577 42.460 1096 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 1021 helix: 1.01 (0.25), residues: 462 sheet: -1.83 (0.48), residues: 114 loop : -3.14 (0.26), residues: 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.1692 time to fit residues: 42.8535 Evaluate side-chains 134 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0774 time to fit residues: 1.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 55 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 ASN ** A 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7994 Z= 0.203 Angle : 0.780 15.366 10866 Z= 0.371 Chirality : 0.044 0.177 1308 Planarity : 0.005 0.083 1372 Dihedral : 5.550 43.320 1096 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.22 % Favored : 90.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 1021 helix: 0.95 (0.25), residues: 463 sheet: -1.87 (0.48), residues: 113 loop : -3.08 (0.26), residues: 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1632 time to fit residues: 40.5762 Evaluate side-chains 131 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 81 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS ** A 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7994 Z= 0.189 Angle : 0.773 15.414 10866 Z= 0.367 Chirality : 0.044 0.177 1308 Planarity : 0.005 0.083 1372 Dihedral : 5.486 42.553 1096 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.43 % Favored : 91.37 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.27), residues: 1021 helix: 1.10 (0.25), residues: 464 sheet: -1.68 (0.49), residues: 111 loop : -3.04 (0.26), residues: 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.1653 time to fit residues: 39.2664 Evaluate side-chains 127 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0854 time to fit residues: 1.7091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 81 optimal weight: 0.0170 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 0.0030 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.0040 overall best weight: 0.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 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 = 0.3852 r_free = 0.3852 target = 0.146641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114255 restraints weight = 19486.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112222 restraints weight = 10745.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113260 restraints weight = 9250.150| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7994 Z= 0.178 Angle : 0.765 15.216 10866 Z= 0.359 Chirality : 0.043 0.180 1308 Planarity : 0.005 0.080 1372 Dihedral : 5.267 41.336 1096 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 2.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.27), residues: 1021 helix: 1.24 (0.25), residues: 456 sheet: -1.50 (0.50), residues: 111 loop : -3.05 (0.26), residues: 454 =============================================================================== Job complete usr+sys time: 1681.60 seconds wall clock time: 31 minutes 15.29 seconds (1875.29 seconds total)