Starting phenix.real_space_refine on Sat Dec 9 01:12:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/12_2023/8seb_40409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/12_2023/8seb_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_40409/12_2023/8seb_40409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/12_2023/8seb_40409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/12_2023/8seb_40409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/12_2023/8seb_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.57, per 1000 atoms: 0.58 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: 4.09 Conformation dependent library (CDL) restraints added in 2.1 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: 3.15 Time building geometry restraints manager: 4.27 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: 0.010 Normalize map: mean=0, sd=1: 2.420 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: 10.100 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.450 Find NCS groups from input model: 0.270 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.170 ------------------------------------------------------------------------------- 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 : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 177 average time/residue: 0.2476 time to fit residues: 59.5822 Evaluate side-chains 95 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0896 time to fit residues: 2.5491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 132 GLN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS A 433 GLN A 480 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9851 Z= 0.301 Angle : 0.595 7.248 13419 Z= 0.287 Chirality : 0.041 0.179 1496 Planarity : 0.004 0.048 1762 Dihedral : 5.943 124.591 1326 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 2.71 % Allowed : 11.88 % Favored : 85.41 % 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: 0.46 (0.25), residues: 1217 helix: 1.40 (0.24), residues: 450 sheet: 0.01 (0.38), residues: 185 loop : -0.40 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.009 0.001 HIS A 142 PHE 0.011 0.001 PHE A 881 TYR 0.015 0.001 TYR C 21 ARG 0.007 0.001 ARG C 118 *********************** 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 127 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 118 average time/residue: 0.2312 time to fit residues: 38.6545 Evaluate side-chains 99 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1275 time to fit residues: 4.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1644 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 : 0.545 7.123 13419 Z= 0.258 Chirality : 0.039 0.177 1496 Planarity : 0.004 0.046 1762 Dihedral : 5.582 97.325 1326 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 1.35 % Allowed : 13.04 % Favored : 85.60 % 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: 0.58 (0.25), residues: 1217 helix: 1.56 (0.25), residues: 451 sheet: -0.06 (0.37), residues: 187 loop : -0.34 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.005 0.001 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.014 0.001 TYR A1010 ARG 0.006 0.000 ARG A 195 *********************** 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 109 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 105 average time/residue: 0.2371 time to fit residues: 34.9452 Evaluate side-chains 96 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0929 time to fit residues: 2.3747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.0070 chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 739 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1888 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= 0.227 Angle : 0.560 8.982 13419 Z= 0.266 Chirality : 0.039 0.225 1496 Planarity : 0.004 0.045 1762 Dihedral : 5.044 67.838 1326 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 2.03 % Allowed : 13.43 % 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: 0.50 (0.25), residues: 1217 helix: 1.50 (0.25), residues: 449 sheet: -0.05 (0.37), residues: 192 loop : -0.41 (0.27), residues: 576 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 0.010 0.001 PHE C 63 TYR 0.019 0.001 TYR C 21 ARG 0.009 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 114 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 107 average time/residue: 0.2401 time to fit residues: 36.6689 Evaluate side-chains 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0922 time to fit residues: 3.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 739 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2101 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= 0.237 Angle : 0.581 9.274 13419 Z= 0.272 Chirality : 0.040 0.251 1496 Planarity : 0.004 0.043 1762 Dihedral : 4.566 47.036 1326 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 1.45 % Allowed : 14.88 % Favored : 83.67 % 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: 0.46 (0.25), residues: 1217 helix: 1.45 (0.25), residues: 449 sheet: -0.21 (0.37), residues: 187 loop : -0.37 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.005 0.001 HIS A 739 PHE 0.011 0.001 PHE C 63 TYR 0.016 0.001 TYR C 21 ARG 0.006 0.000 ARG A 942 *********************** 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 104 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 0.2155 time to fit residues: 31.6585 Evaluate side-chains 91 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0952 time to fit residues: 2.5616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 0.0270 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 overall best weight: 0.4454 ------------------------------------------------------------------------------- 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: 0.7030 moved from start: 0.2174 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= 0.160 Angle : 0.564 9.958 13419 Z= 0.262 Chirality : 0.040 0.254 1496 Planarity : 0.004 0.043 1762 Dihedral : 4.314 45.316 1326 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 1.26 % Allowed : 15.94 % Favored : 82.80 % 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: 0.54 (0.25), residues: 1217 helix: 1.54 (0.25), residues: 449 sheet: -0.15 (0.37), residues: 188 loop : -0.34 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.003 0.000 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.019 0.001 TYR C 21 ARG 0.008 0.000 ARG A 204 *********************** 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 102 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 0.2253 time to fit residues: 30.9660 Evaluate side-chains 88 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1042 time to fit residues: 2.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 85 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2403 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= 0.291 Angle : 0.604 7.764 13419 Z= 0.287 Chirality : 0.041 0.221 1496 Planarity : 0.004 0.044 1762 Dihedral : 4.460 45.633 1326 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 0.58 % Allowed : 16.33 % Favored : 83.09 % 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: 1.39 (0.25), residues: 447 sheet: -0.27 (0.37), residues: 188 loop : -0.37 (0.27), residues: 582 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 0.014 0.001 TYR C 21 ARG 0.003 0.000 ARG B 99 *********************** 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 93 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.2495 time to fit residues: 33.6053 Evaluate side-chains 85 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1049 time to fit residues: 2.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7048 moved from start: 0.2443 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= 0.188 Angle : 0.578 10.562 13419 Z= 0.270 Chirality : 0.040 0.230 1496 Planarity : 0.004 0.043 1762 Dihedral : 4.311 45.079 1326 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 0.68 % Allowed : 16.23 % Favored : 83.09 % 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: 0.54 (0.25), residues: 1217 helix: 1.50 (0.25), residues: 447 sheet: -0.19 (0.37), residues: 188 loop : -0.29 (0.27), residues: 582 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 0.022 0.001 TYR C 21 ARG 0.004 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 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.119 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.2539 time to fit residues: 32.9937 Evaluate side-chains 90 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1143 time to fit residues: 2.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 30.0000 chunk 47 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2491 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= 0.186 Angle : 0.591 13.747 13419 Z= 0.274 Chirality : 0.040 0.243 1496 Planarity : 0.004 0.044 1762 Dihedral : 4.294 45.321 1326 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 0.39 % Allowed : 16.52 % Favored : 83.09 % 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: 0.57 (0.25), residues: 1217 helix: 1.54 (0.25), residues: 447 sheet: -0.17 (0.37), residues: 188 loop : -0.28 (0.27), residues: 582 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 0.010 0.001 PHE C 63 TYR 0.020 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 97 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.978 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.2426 time to fit residues: 33.2039 Evaluate side-chains 92 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1041 time to fit residues: 2.0831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7055 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9851 Z= 0.236 Angle : 0.604 13.490 13419 Z= 0.281 Chirality : 0.041 0.283 1496 Planarity : 0.004 0.038 1762 Dihedral : 4.360 45.921 1326 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 0.19 % Allowed : 16.62 % Favored : 83.19 % 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: 0.48 (0.25), residues: 1217 helix: 1.46 (0.25), residues: 447 sheet: -0.21 (0.37), residues: 188 loop : -0.33 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 666 HIS 0.003 0.001 HIS A 142 PHE 0.016 0.001 PHE C 136 TYR 0.026 0.001 TYR B 140 ARG 0.003 0.000 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 91 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.178 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.2902 time to fit residues: 37.5543 Evaluate side-chains 88 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0889 time to fit residues: 1.7536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.213121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139851 restraints weight = 12619.528| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.68 r_work: 0.3407 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9851 Z= 0.196 Angle : 0.593 13.040 13419 Z= 0.276 Chirality : 0.041 0.435 1496 Planarity : 0.004 0.039 1762 Dihedral : 4.332 45.725 1326 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 0.39 % Allowed : 16.91 % Favored : 82.71 % 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: 1.51 (0.25), residues: 448 sheet: -0.12 (0.38), residues: 188 loop : -0.33 (0.27), residues: 581 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 0.017 0.001 PHE C 136 TYR 0.018 0.001 TYR C 21 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: 2366.94 seconds wall clock time: 43 minutes 51.96 seconds (2631.96 seconds total)