Starting phenix.real_space_refine on Thu Mar 14 19:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/03_2024/8seb_40409_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 36 5.16 5 C 6106 2.51 5 N 1687 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.55 Number of scatterers: 9609 At special positions: 0 Unit cell: (103.317, 96.6512, 112.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 1 15.00 O 1779 8.00 N 1687 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 37.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.731A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.874A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.885A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 304 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 526 through 529 No H-bonds generated for 'chain 'A' and resid 526 through 529' Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 586 through 592 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 608 through 622 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 644 through 655 removed outlier: 3.540A pdb=" N GLN A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 649 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A 653 " --> pdb=" O THR A 650 " (cutoff:3.500A) Proline residue: A 654 - end of helix Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.915A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 722 through 738 Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 784 through 798 removed outlier: 3.779A pdb=" N LYS A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 817 through 831 removed outlier: 3.684A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 844 removed outlier: 3.662A pdb=" N ARG A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 871 removed outlier: 3.721A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 939 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.688A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 133 through 147 Processing sheet with id= A, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 58 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A 37 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 60 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN A 103 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 61 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 105 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.679A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= D, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.508A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 892 through 896 removed outlier: 6.218A pdb=" N LEU A 436 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A 538 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 438 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A 465 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 904 through 906 Processing sheet with id= G, first strand: chain 'A' and resid 917 through 920 Processing sheet with id= H, first strand: chain 'A' and resid 993 through 996 removed outlier: 3.502A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU A 952 " --> pdb=" O HIS A 948 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 93 through 98 Processing sheet with id= J, first strand: chain 'C' and resid 34 through 39 344 hydrogen bonds defined for protein. 963 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: 3.02 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1466 1.45 - 1.57: 5473 1.57 - 1.69: 4 1.69 - 1.81: 54 Bond restraints: 9851 Sorted by residual: bond pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.415 1.621 -0.206 1.50e-02 4.44e+03 1.88e+02 bond pdb=" C1' AMP B 201 " pdb=" C2' AMP B 201 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.18e+02 bond pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.454 1.292 0.162 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C6 AMP B 201 " pdb=" N6 AMP B 201 " ideal model delta sigma weight residual 1.355 1.496 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4 AMP B 201 " pdb=" C5 AMP B 201 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 9846 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.93: 203 103.93 - 111.66: 4666 111.66 - 119.39: 3630 119.39 - 127.12: 4754 127.12 - 134.85: 166 Bond angle restraints: 13419 Sorted by residual: angle pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" N9 AMP B 201 " ideal model delta sigma weight residual 114.00 127.40 -13.40 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N9 AMP B 201 " pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 108.20 96.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C4' AMP B 201 " ideal model delta sigma weight residual 109.70 101.81 7.89 1.00e+00 1.00e+00 6.22e+01 angle pdb=" O2P AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sigma weight residual 119.90 105.09 14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C3' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sigma weight residual 115.20 109.40 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 13414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 5800 29.88 - 59.77: 128 59.77 - 89.65: 10 89.65 - 119.54: 0 119.54 - 149.42: 1 Dihedral angle restraints: 5939 sinusoidal: 2399 harmonic: 3540 Sorted by residual: dihedral pdb=" C5' AMP B 201 " pdb=" O5' AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sinusoidal sigma weight residual 300.00 150.58 149.42 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C1' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sinusoidal sigma weight residual -123.00 -156.55 33.55 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 855 0.025 - 0.050: 407 0.050 - 0.074: 123 0.074 - 0.099: 77 0.099 - 0.124: 34 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" C3' AMP B 201 " pdb=" O2' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.52 -2.40 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1493 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 645 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 646 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 518 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 692 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 693 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 693 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 693 " -0.017 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1107 2.75 - 3.29: 9897 3.29 - 3.83: 16118 3.83 - 4.36: 18769 4.36 - 4.90: 32210 Nonbonded interactions: 78101 Sorted by model distance: nonbonded pdb=" OG1 THR A 927 " pdb=" O LEU A 967 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASP A 517 " pdb=" OG1 THR A 519 " model vdw 2.231 2.440 nonbonded pdb=" O THR A 553 " pdb=" NH2 ARG A 916 " model vdw 2.264 2.520 nonbonded pdb=" O GLU A 621 " pdb=" OG SER A 626 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THR C 99 " pdb=" OE1 GLN C 103 " model vdw 2.277 2.440 ... (remaining 78096 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 10.010 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.890 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.005 0.206 9851 Z= 0.297 Angle : 0.583 14.813 13419 Z= 0.305 Chirality : 0.037 0.124 1496 Planarity : 0.004 0.053 1762 Dihedral : 12.083 149.425 3644 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 8.02 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1217 helix: 1.62 (0.25), residues: 448 sheet: 0.19 (0.39), residues: 182 loop : -0.34 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.002 0.000 HIS A 817 PHE 0.008 0.001 PHE A 146 TYR 0.007 0.001 TYR A 388 ARG 0.002 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 177 LEU cc_start: 0.6400 (mm) cc_final: 0.5709 (mt) REVERT: A 224 ASP cc_start: 0.8906 (m-30) cc_final: 0.8695 (p0) REVERT: A 229 HIS cc_start: 0.6930 (t-90) cc_final: 0.6423 (t-90) REVERT: A 256 VAL cc_start: 0.8355 (t) cc_final: 0.7773 (m) REVERT: A 258 ARG cc_start: 0.7278 (ptp-110) cc_final: 0.6752 (mtt-85) REVERT: A 410 LEU cc_start: 0.8792 (mp) cc_final: 0.8499 (mt) REVERT: A 473 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 476 ASN cc_start: 0.7845 (m110) cc_final: 0.7611 (m-40) REVERT: A 490 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8209 (mtm110) REVERT: A 565 SER cc_start: 0.8111 (t) cc_final: 0.7471 (p) REVERT: A 738 MET cc_start: -0.0859 (mtp) cc_final: -0.1281 (mpp) REVERT: A 867 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 988 ARG cc_start: 0.7076 (mmp-170) cc_final: 0.6728 (mmp80) REVERT: B 87 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 26 SER cc_start: 0.7760 (p) cc_final: 0.7399 (t) REVERT: C 67 MET cc_start: 0.7287 (mpp) cc_final: 0.7021 (mpp) REVERT: C 136 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5768 (m-80) outliers start: 18 outliers final: 6 residues processed: 177 average time/residue: 0.2410 time to fit residues: 58.3647 Evaluate side-chains 104 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS A 433 GLN A 508 GLN A 831 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9851 Z= 0.342 Angle : 0.619 7.269 13419 Z= 0.300 Chirality : 0.041 0.173 1496 Planarity : 0.004 0.048 1762 Dihedral : 6.489 115.525 1337 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 3.09 % Allowed : 11.01 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1217 helix: 1.30 (0.24), residues: 447 sheet: -0.23 (0.37), residues: 186 loop : -0.45 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.008 0.001 HIS A 142 PHE 0.012 0.002 PHE A 881 TYR 0.013 0.002 TYR A1010 ARG 0.008 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7867 (mmm) cc_final: 0.7351 (mmm) REVERT: A 58 SER cc_start: 0.8488 (t) cc_final: 0.7799 (m) REVERT: A 84 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 224 ASP cc_start: 0.8976 (m-30) cc_final: 0.8762 (p0) REVERT: A 229 HIS cc_start: 0.7055 (t-90) cc_final: 0.6516 (t-90) REVERT: A 256 VAL cc_start: 0.8557 (t) cc_final: 0.8093 (m) REVERT: A 258 ARG cc_start: 0.7269 (ptp-110) cc_final: 0.6719 (mtt-85) REVERT: A 410 LEU cc_start: 0.8729 (mp) cc_final: 0.8525 (mt) REVERT: A 477 LEU cc_start: 0.7807 (pt) cc_final: 0.7565 (pt) REVERT: A 480 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7750 (mp10) REVERT: A 738 MET cc_start: -0.0935 (mtp) cc_final: -0.1351 (mpp) REVERT: A 988 ARG cc_start: 0.7277 (mmp-170) cc_final: 0.6938 (mmp80) REVERT: B 87 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7542 (tpp80) REVERT: B 107 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7746 (tp) REVERT: C 26 SER cc_start: 0.7856 (p) cc_final: 0.7541 (t) REVERT: C 54 ARG cc_start: 0.6546 (ttm170) cc_final: 0.6034 (ptm160) REVERT: C 136 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5872 (m-80) outliers start: 32 outliers final: 18 residues processed: 128 average time/residue: 0.2352 time to fit residues: 41.9765 Evaluate side-chains 113 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 118 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 157 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9851 Z= 0.148 Angle : 0.535 7.117 13419 Z= 0.252 Chirality : 0.039 0.150 1496 Planarity : 0.004 0.046 1762 Dihedral : 5.846 90.449 1334 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 2.90 % Allowed : 12.56 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1217 helix: 1.55 (0.25), residues: 451 sheet: -0.26 (0.37), residues: 188 loop : -0.33 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.004 0.000 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.015 0.001 TYR A1010 ARG 0.007 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7816 (mmm) cc_final: 0.7376 (mmm) REVERT: A 58 SER cc_start: 0.8361 (t) cc_final: 0.7611 (m) REVERT: A 84 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 229 HIS cc_start: 0.6992 (t-90) cc_final: 0.6427 (t-90) REVERT: A 256 VAL cc_start: 0.8619 (t) cc_final: 0.8213 (m) REVERT: A 258 ARG cc_start: 0.7216 (ptp-110) cc_final: 0.6683 (mtt-85) REVERT: A 477 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7580 (pt) REVERT: A 480 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7701 (mp10) REVERT: A 565 SER cc_start: 0.7919 (t) cc_final: 0.7306 (p) REVERT: A 738 MET cc_start: -0.0879 (mtp) cc_final: -0.1305 (mpp) REVERT: A 988 ARG cc_start: 0.7185 (mmp-170) cc_final: 0.6873 (mmp80) REVERT: B 87 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7495 (tpp80) REVERT: B 155 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6927 (ptp-170) REVERT: C 26 SER cc_start: 0.7855 (p) cc_final: 0.7548 (t) REVERT: C 54 ARG cc_start: 0.6451 (ttm170) cc_final: 0.6073 (ptm160) REVERT: C 103 GLN cc_start: 0.7688 (mt0) cc_final: 0.7091 (tp40) REVERT: C 136 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5820 (m-80) outliers start: 30 outliers final: 15 residues processed: 132 average time/residue: 0.2436 time to fit residues: 44.7040 Evaluate side-chains 115 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9851 Z= 0.257 Angle : 0.576 9.321 13419 Z= 0.273 Chirality : 0.040 0.235 1496 Planarity : 0.004 0.045 1762 Dihedral : 5.437 60.160 1334 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 3.57 % Allowed : 13.04 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1217 helix: 1.47 (0.25), residues: 450 sheet: -0.40 (0.37), residues: 189 loop : -0.38 (0.28), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.004 0.001 HIS B 106 PHE 0.013 0.001 PHE A 881 TYR 0.018 0.001 TYR C 21 ARG 0.008 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7777 (mmm) cc_final: 0.7290 (mmm) REVERT: A 58 SER cc_start: 0.8464 (t) cc_final: 0.7761 (m) REVERT: A 84 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 229 HIS cc_start: 0.7017 (t-90) cc_final: 0.6458 (t-90) REVERT: A 256 VAL cc_start: 0.8684 (t) cc_final: 0.8287 (m) REVERT: A 258 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6731 (mtt-85) REVERT: A 477 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7574 (pt) REVERT: A 480 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7727 (mp10) REVERT: A 503 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7149 (tt) REVERT: A 565 SER cc_start: 0.7966 (t) cc_final: 0.7376 (p) REVERT: A 738 MET cc_start: -0.0724 (mtp) cc_final: -0.1181 (mpp) REVERT: A 988 ARG cc_start: 0.7194 (mmp-170) cc_final: 0.6865 (mmp80) REVERT: B 87 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7502 (tpp80) REVERT: C 26 SER cc_start: 0.7985 (p) cc_final: 0.7662 (t) REVERT: C 54 ARG cc_start: 0.6391 (ttm170) cc_final: 0.6007 (ptt90) REVERT: C 136 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5741 (m-80) outliers start: 37 outliers final: 24 residues processed: 126 average time/residue: 0.2316 time to fit residues: 41.2928 Evaluate side-chains 120 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9851 Z= 0.277 Angle : 0.582 8.636 13419 Z= 0.275 Chirality : 0.040 0.224 1496 Planarity : 0.004 0.042 1762 Dihedral : 5.073 50.232 1334 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 4.06 % Allowed : 13.62 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1217 helix: 1.30 (0.25), residues: 450 sheet: -0.54 (0.36), residues: 189 loop : -0.42 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.003 0.001 HIS A 142 PHE 0.011 0.001 PHE C 63 TYR 0.017 0.001 TYR C 21 ARG 0.010 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7799 (mmm) cc_final: 0.7298 (mmm) REVERT: A 58 SER cc_start: 0.8495 (t) cc_final: 0.7818 (m) REVERT: A 84 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 256 VAL cc_start: 0.8642 (t) cc_final: 0.8259 (m) REVERT: A 258 ARG cc_start: 0.7305 (ptp-110) cc_final: 0.6806 (mtt-85) REVERT: A 477 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7624 (pt) REVERT: A 480 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7750 (mp10) REVERT: A 503 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7197 (tt) REVERT: A 565 SER cc_start: 0.7970 (t) cc_final: 0.7373 (p) REVERT: A 738 MET cc_start: -0.0700 (mtp) cc_final: -0.1124 (mpp) REVERT: A 988 ARG cc_start: 0.7210 (mmp-170) cc_final: 0.6880 (mmp80) REVERT: B 87 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7560 (tpp80) REVERT: C 26 SER cc_start: 0.8080 (p) cc_final: 0.7745 (t) REVERT: C 54 ARG cc_start: 0.6383 (ttm170) cc_final: 0.6013 (ptm160) REVERT: C 57 PHE cc_start: 0.7991 (m-80) cc_final: 0.7620 (m-80) REVERT: C 136 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5769 (m-80) outliers start: 42 outliers final: 29 residues processed: 127 average time/residue: 0.2260 time to fit residues: 40.5369 Evaluate side-chains 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 117 optimal weight: 0.0370 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9851 Z= 0.180 Angle : 0.551 9.353 13419 Z= 0.257 Chirality : 0.039 0.238 1496 Planarity : 0.004 0.040 1762 Dihedral : 4.807 49.000 1334 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 3.48 % Allowed : 14.59 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1217 helix: 1.53 (0.25), residues: 448 sheet: -0.47 (0.37), residues: 188 loop : -0.38 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.003 0.000 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.014 0.001 TYR C 21 ARG 0.006 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7724 (mmm) cc_final: 0.7245 (mmm) REVERT: A 58 SER cc_start: 0.8412 (t) cc_final: 0.7717 (m) REVERT: A 84 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 256 VAL cc_start: 0.8660 (t) cc_final: 0.8289 (m) REVERT: A 258 ARG cc_start: 0.7246 (ptp-110) cc_final: 0.6731 (mtt-85) REVERT: A 477 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7584 (pt) REVERT: A 503 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 565 SER cc_start: 0.7962 (t) cc_final: 0.7340 (p) REVERT: A 738 MET cc_start: -0.0721 (mtp) cc_final: -0.1149 (mpp) REVERT: A 988 ARG cc_start: 0.7131 (mmp-170) cc_final: 0.6807 (mmp80) REVERT: B 87 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7575 (tpp80) REVERT: C 26 SER cc_start: 0.8098 (p) cc_final: 0.7777 (t) REVERT: C 54 ARG cc_start: 0.6304 (ttm170) cc_final: 0.5987 (ptm160) REVERT: C 103 GLN cc_start: 0.7706 (mt0) cc_final: 0.7109 (tp40) REVERT: C 136 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5682 (m-80) outliers start: 36 outliers final: 24 residues processed: 125 average time/residue: 0.2236 time to fit residues: 39.5906 Evaluate side-chains 117 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 98 optimal weight: 0.0030 chunk 65 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9851 Z= 0.308 Angle : 0.607 9.768 13419 Z= 0.291 Chirality : 0.041 0.246 1496 Planarity : 0.004 0.042 1762 Dihedral : 5.029 48.200 1334 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.48 % Allowed : 14.40 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1217 helix: 1.37 (0.25), residues: 447 sheet: -0.54 (0.37), residues: 186 loop : -0.42 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.003 0.001 HIS A 434 PHE 0.012 0.001 PHE C 63 TYR 0.020 0.001 TYR C 21 ARG 0.005 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7799 (mmm) cc_final: 0.7279 (mmm) REVERT: A 58 SER cc_start: 0.8533 (t) cc_final: 0.7871 (m) REVERT: A 84 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 256 VAL cc_start: 0.8670 (t) cc_final: 0.8305 (m) REVERT: A 258 ARG cc_start: 0.7324 (ptp-110) cc_final: 0.6813 (mtt-85) REVERT: A 363 MET cc_start: 0.6353 (tpt) cc_final: 0.5892 (tpt) REVERT: A 503 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7224 (tt) REVERT: A 565 SER cc_start: 0.7986 (t) cc_final: 0.7391 (p) REVERT: A 738 MET cc_start: -0.0708 (mtp) cc_final: -0.1123 (mpp) REVERT: A 988 ARG cc_start: 0.7242 (mmp-170) cc_final: 0.6911 (mmp80) REVERT: B 87 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7648 (tpp80) REVERT: B 139 GLU cc_start: 0.8577 (tt0) cc_final: 0.8328 (tt0) REVERT: C 26 SER cc_start: 0.8115 (p) cc_final: 0.7775 (t) REVERT: C 54 ARG cc_start: 0.6375 (ttm170) cc_final: 0.6033 (ptm160) REVERT: C 57 PHE cc_start: 0.7979 (m-80) cc_final: 0.7623 (m-80) outliers start: 36 outliers final: 31 residues processed: 120 average time/residue: 0.2178 time to fit residues: 36.7244 Evaluate side-chains 122 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9851 Z= 0.193 Angle : 0.564 10.083 13419 Z= 0.265 Chirality : 0.040 0.250 1496 Planarity : 0.004 0.041 1762 Dihedral : 4.679 45.402 1332 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.09 % Allowed : 14.98 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1217 helix: 1.54 (0.25), residues: 447 sheet: -0.54 (0.37), residues: 188 loop : -0.37 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.003 0.000 HIS A 142 PHE 0.010 0.001 PHE C 63 TYR 0.016 0.001 TYR C 21 ARG 0.006 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7727 (mmm) cc_final: 0.7261 (mmm) REVERT: A 58 SER cc_start: 0.8474 (t) cc_final: 0.7789 (m) REVERT: A 84 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 256 VAL cc_start: 0.8666 (t) cc_final: 0.8306 (m) REVERT: A 258 ARG cc_start: 0.7247 (ptp-110) cc_final: 0.6708 (mtt-85) REVERT: A 503 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7191 (tt) REVERT: A 565 SER cc_start: 0.7968 (t) cc_final: 0.7350 (p) REVERT: A 738 MET cc_start: -0.0620 (mtp) cc_final: -0.1033 (mpp) REVERT: A 988 ARG cc_start: 0.7172 (mmp-170) cc_final: 0.6852 (mmp80) REVERT: B 87 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7601 (tpp80) REVERT: B 139 GLU cc_start: 0.8550 (tt0) cc_final: 0.8308 (tt0) REVERT: C 26 SER cc_start: 0.8140 (p) cc_final: 0.7814 (t) REVERT: C 54 ARG cc_start: 0.6351 (ttm170) cc_final: 0.6145 (ptm-80) REVERT: C 57 PHE cc_start: 0.7952 (m-80) cc_final: 0.7644 (m-80) REVERT: C 103 GLN cc_start: 0.7694 (mt0) cc_final: 0.7113 (tp40) outliers start: 32 outliers final: 30 residues processed: 119 average time/residue: 0.2330 time to fit residues: 38.6255 Evaluate side-chains 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 65 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.227 Angle : 0.578 10.377 13419 Z= 0.273 Chirality : 0.040 0.259 1496 Planarity : 0.004 0.042 1762 Dihedral : 4.690 46.069 1332 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 3.29 % Allowed : 14.88 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1217 helix: 1.55 (0.25), residues: 448 sheet: -0.56 (0.37), residues: 189 loop : -0.40 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 666 HIS 0.003 0.000 HIS A 142 PHE 0.011 0.001 PHE C 63 TYR 0.017 0.001 TYR C 21 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7751 (mmm) cc_final: 0.7293 (mmm) REVERT: A 58 SER cc_start: 0.8474 (t) cc_final: 0.7798 (m) REVERT: A 256 VAL cc_start: 0.8679 (t) cc_final: 0.8319 (m) REVERT: A 258 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6728 (mtt-85) REVERT: A 363 MET cc_start: 0.6280 (tpt) cc_final: 0.5774 (tpt) REVERT: A 503 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7204 (tt) REVERT: A 565 SER cc_start: 0.7970 (t) cc_final: 0.7369 (p) REVERT: A 738 MET cc_start: -0.0498 (mtp) cc_final: -0.0909 (mpp) REVERT: A 988 ARG cc_start: 0.7182 (mmp-170) cc_final: 0.6861 (mmp80) REVERT: B 139 GLU cc_start: 0.8589 (tt0) cc_final: 0.8331 (tt0) REVERT: C 26 SER cc_start: 0.8147 (p) cc_final: 0.7821 (t) REVERT: C 57 PHE cc_start: 0.7976 (m-80) cc_final: 0.7664 (m-80) REVERT: C 89 ILE cc_start: 0.8127 (mm) cc_final: 0.7901 (mp) outliers start: 34 outliers final: 31 residues processed: 123 average time/residue: 0.2301 time to fit residues: 40.2308 Evaluate side-chains 125 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9851 Z= 0.368 Angle : 0.638 10.259 13419 Z= 0.306 Chirality : 0.042 0.283 1496 Planarity : 0.004 0.044 1762 Dihedral : 5.014 46.834 1332 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 3.57 % Allowed : 14.98 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1217 helix: 1.24 (0.24), residues: 447 sheet: -0.68 (0.37), residues: 184 loop : -0.55 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 666 HIS 0.004 0.001 HIS A 201 PHE 0.012 0.001 PHE C 63 TYR 0.016 0.002 TYR C 21 ARG 0.006 0.001 ARG A 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.7796 (mmm) cc_final: 0.7249 (mmm) REVERT: A 58 SER cc_start: 0.8594 (t) cc_final: 0.7956 (m) REVERT: A 217 MET cc_start: 0.4137 (mpp) cc_final: 0.3895 (mmt) REVERT: A 256 VAL cc_start: 0.8673 (t) cc_final: 0.8314 (m) REVERT: A 258 ARG cc_start: 0.7318 (ptp-110) cc_final: 0.6800 (mtt-85) REVERT: A 503 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 738 MET cc_start: -0.0501 (mtp) cc_final: -0.0897 (mpp) REVERT: A 988 ARG cc_start: 0.7244 (mmp-170) cc_final: 0.6906 (mmp80) REVERT: B 139 GLU cc_start: 0.8644 (tt0) cc_final: 0.8376 (tt0) REVERT: C 26 SER cc_start: 0.8176 (p) cc_final: 0.7831 (t) REVERT: C 57 PHE cc_start: 0.7992 (m-80) cc_final: 0.7610 (m-80) REVERT: C 89 ILE cc_start: 0.8160 (mm) cc_final: 0.7917 (mp) outliers start: 37 outliers final: 33 residues processed: 120 average time/residue: 0.2218 time to fit residues: 37.5798 Evaluate side-chains 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 69 optimal weight: 0.0000 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 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 = 0.4572 r_free = 0.4572 target = 0.212869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140869 restraints weight = 12588.345| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.93 r_work: 0.3421 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9851 Z= 0.156 Angle : 0.564 10.620 13419 Z= 0.264 Chirality : 0.039 0.262 1496 Planarity : 0.004 0.041 1762 Dihedral : 4.554 45.083 1332 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 2.71 % Allowed : 15.65 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1217 helix: 1.67 (0.25), residues: 447 sheet: -0.49 (0.38), residues: 178 loop : -0.39 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 666 HIS 0.005 0.001 HIS A 522 PHE 0.009 0.001 PHE C 63 TYR 0.011 0.001 TYR A1010 ARG 0.004 0.000 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2346.46 seconds wall clock time: 42 minutes 37.44 seconds (2557.44 seconds total)