Starting phenix.real_space_refine on Mon Mar 11 08:26:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/03_2024/8ien_35387_trim_updated.pdb" } resolution = 3.25 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= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 4959 2.51 5 N 1320 2.21 5 O 1340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 235": "OE1" <-> "OE2" Residue "P GLU 303": "OE1" <-> "OE2" Residue "P GLU 348": "OE1" <-> "OE2" Residue "P GLU 367": "OE1" <-> "OE2" Residue "P GLU 520": "OE1" <-> "OE2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P GLU 782": "OE1" <-> "OE2" Residue "P GLU 861": "OE1" <-> "OE2" Residue "P GLU 1135": "OE1" <-> "OE2" 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: 7678 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7644 Classifications: {'peptide': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 65, 'TRANS': 922} Chain breaks: 6 Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.37, per 1000 atoms: 0.57 Number of scatterers: 7678 At special positions: 0 Unit cell: (86.505, 112.785, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1340 8.00 N 1320 7.00 C 4959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 43.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'P' and resid 51 through 58 Processing helix chain 'P' and resid 61 through 65 Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.828A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 200 Processing helix chain 'P' and resid 209 through 216 Processing helix chain 'P' and resid 228 through 235 Processing helix chain 'P' and resid 239 through 253 Processing helix chain 'P' and resid 257 through 289 Processing helix chain 'P' and resid 309 through 311 No H-bonds generated for 'chain 'P' and resid 309 through 311' Processing helix chain 'P' and resid 404 through 412 removed outlier: 4.003A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 450 removed outlier: 3.719A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 457 through 468 removed outlier: 3.910A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) Processing helix chain 'P' and resid 473 through 491 removed outlier: 4.347A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR P 481 " --> pdb=" O MET P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 505 removed outlier: 3.815A pdb=" N ASN P 502 " --> pdb=" O LEU P 499 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY P 505 " --> pdb=" O ASN P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 550 through 557 Processing helix chain 'P' and resid 572 through 580 Processing helix chain 'P' and resid 657 through 665 removed outlier: 3.604A pdb=" N ASN P 665 " --> pdb=" O ALA P 661 " (cutoff:3.500A) Processing helix chain 'P' and resid 674 through 682 Processing helix chain 'P' and resid 730 through 741 Proline residue: P 734 - end of helix Processing helix chain 'P' and resid 754 through 764 Processing helix chain 'P' and resid 827 through 836 removed outlier: 3.540A pdb=" N HIS P 836 " --> pdb=" O ILE P 832 " (cutoff:3.500A) Processing helix chain 'P' and resid 841 through 847 Processing helix chain 'P' and resid 856 through 869 removed outlier: 3.665A pdb=" N LEU P 869 " --> pdb=" O GLU P 865 " (cutoff:3.500A) Processing helix chain 'P' and resid 881 through 888 removed outlier: 4.440A pdb=" N GLY P 884 " --> pdb=" O ASN P 881 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA P 888 " --> pdb=" O ALA P 885 " (cutoff:3.500A) Processing helix chain 'P' and resid 913 through 954 removed outlier: 3.571A pdb=" N VAL P 916 " --> pdb=" O ILE P 913 " (cutoff:3.500A) Proline residue: P 917 - end of helix Processing helix chain 'P' and resid 960 through 969 Processing helix chain 'P' and resid 971 through 977 Processing helix chain 'P' and resid 999 through 1025 removed outlier: 3.750A pdb=" N LEU P1017 " --> pdb=" O THR P1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P1018 " --> pdb=" O GLY P1014 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P1019 " --> pdb=" O VAL P1015 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR P1020 " --> pdb=" O GLN P1016 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1038 through 1040 No H-bonds generated for 'chain 'P' and resid 1038 through 1040' Processing helix chain 'P' and resid 1045 through 1064 removed outlier: 3.618A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1079 through 1097 Processing helix chain 'P' and resid 1114 through 1140 removed outlier: 3.988A pdb=" N GLN P1140 " --> pdb=" O SER P1136 " (cutoff:3.500A) Processing helix chain 'P' and resid 1142 through 1145 No H-bonds generated for 'chain 'P' and resid 1142 through 1145' Processing helix chain 'P' and resid 1157 through 1168 Processing sheet with id= A, first strand: chain 'P' and resid 88 through 90 Processing sheet with id= B, first strand: chain 'P' and resid 165 through 168 removed outlier: 3.501A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 294 through 299 removed outlier: 3.843A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 351 through 354 removed outlier: 3.770A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'P' and resid 493 through 495 Processing sheet with id= F, first strand: chain 'P' and resid 509 through 512 removed outlier: 6.987A pdb=" N ARG P 745 " --> pdb=" O VAL P 510 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N PHE P 512 " --> pdb=" O ARG P 745 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL P 747 " --> pdb=" O PHE P 512 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'P' and resid 717 through 723 removed outlier: 7.360A pdb=" N LEU P 690 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU P 721 " --> pdb=" O VAL P 688 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL P 688 " --> pdb=" O LEU P 721 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA P 689 " --> pdb=" O GLY P 655 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'P' and resid 874 through 877 removed outlier: 6.345A pdb=" N VAL P 891 " --> pdb=" O MET P 875 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLY P 877 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE P 893 " --> pdb=" O GLY P 877 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'P' and resid 330 through 333 removed outlier: 3.599A pdb=" N ASP P 330 " --> pdb=" O ARG P 397 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG P 397 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA P 332 " --> pdb=" O VAL P 395 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL P 395 " --> pdb=" O ALA P 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'P' and resid 823 through 825 removed outlier: 7.224A pdb=" N LEU P 825 " --> pdb=" O THR P 849 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE P 851 " --> pdb=" O LEU P 825 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2449 1.35 - 1.46: 1687 1.46 - 1.58: 3623 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7842 Sorted by residual: bond pdb=" C11 SPM P1204 " pdb=" C12 SPM P1204 " ideal model delta sigma weight residual 1.527 1.395 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C12 SPM P1204 " pdb=" C13 SPM P1204 " ideal model delta sigma weight residual 1.527 1.407 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 89.99 - 107.99: 391 107.99 - 125.99: 10137 125.99 - 143.99: 139 143.99 - 162.00: 0 162.00 - 180.00: 2 Bond angle restraints: 10669 Sorted by residual: angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F2 ALF P1202 " ideal model delta sigma weight residual 108.68 179.98 -71.30 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 109.63 180.00 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.69 90.01 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.59 90.01 19.58 3.00e+00 1.11e-01 4.26e+01 ... (remaining 10664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4247 17.68 - 35.35: 401 35.35 - 53.03: 71 53.03 - 70.70: 16 70.70 - 88.38: 5 Dihedral angle restraints: 4740 sinusoidal: 1880 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ASP P 189 " pdb=" CB ASP P 189 " pdb=" CG ASP P 189 " pdb=" OD1 ASP P 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU P 650 " pdb=" CG GLU P 650 " pdb=" CD GLU P 650 " pdb=" OE1 GLU P 650 " ideal model delta sinusoidal sigma weight residual 0.00 88.38 -88.38 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 996 0.044 - 0.088: 197 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA SER P 425 " pdb=" N SER P 425 " pdb=" C SER P 425 " pdb=" CB SER P 425 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS P 424 " pdb=" N HIS P 424 " pdb=" C HIS P 424 " pdb=" CB HIS P 424 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PRO P 618 " pdb=" N PRO P 618 " pdb=" C PRO P 618 " pdb=" CB PRO P 618 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1263 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO P 618 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO P 619 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 426 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET P 426 " -0.030 2.00e-02 2.50e+03 pdb=" O MET P 426 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS P 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P1042 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO P1043 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO P1043 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1043 " -0.019 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 219 2.71 - 3.26: 7475 3.26 - 3.81: 12015 3.81 - 4.35: 14202 4.35 - 4.90: 24075 Nonbonded interactions: 57986 Sorted by model distance: nonbonded pdb="MG MG P1201 " pdb=" F1 ALF P1202 " model vdw 2.168 2.120 nonbonded pdb=" CG2 VAL P 467 " pdb=" C12 SPM P1204 " model vdw 2.241 3.860 nonbonded pdb=" OD2 ASP P 513 " pdb="MG MG P1201 " model vdw 2.252 2.170 nonbonded pdb=" O THR P 515 " pdb="MG MG P1201 " model vdw 2.280 2.170 nonbonded pdb=" CZ3 TRP P 251 " pdb=" C9 SPM P1204 " model vdw 2.282 3.740 ... (remaining 57981 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: 1.510 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: 6.050 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 23.730 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 7842 Z= 0.282 Angle : 1.211 71.295 10669 Z= 0.486 Chirality : 0.040 0.220 1266 Planarity : 0.004 0.050 1339 Dihedral : 14.043 88.379 2894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -2.18 (0.25), residues: 977 helix: -0.46 (0.23), residues: 450 sheet: -1.34 (0.62), residues: 61 loop : -2.50 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 PHE 0.015 0.001 PHE P1128 TYR 0.015 0.001 TYR P 256 ARG 0.002 0.000 ARG P1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2586 (pt) REVERT: P 326 LEU cc_start: 0.3219 (tp) cc_final: 0.2997 (pp) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1444 (tpp) REVERT: P 577 MET cc_start: 0.1892 (mtp) cc_final: 0.0826 (tmm) REVERT: P 637 MET cc_start: 0.1190 (tmm) cc_final: 0.0942 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.1770 time to fit residues: 21.3889 Evaluate side-chains 55 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 77 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS P 219 ASN P 281 GLN P 559 HIS ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0525 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7842 Z= 0.175 Angle : 0.880 30.381 10669 Z= 0.358 Chirality : 0.040 0.142 1266 Planarity : 0.005 0.045 1339 Dihedral : 5.683 57.639 1095 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.24 % Allowed : 9.23 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.24 (0.26), residues: 977 helix: 0.31 (0.24), residues: 443 sheet: -0.44 (0.55), residues: 89 loop : -2.12 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 251 HIS 0.003 0.001 HIS P 424 PHE 0.012 0.001 PHE P1128 TYR 0.018 0.001 TYR P 483 ARG 0.004 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3031 (mt) cc_final: 0.2748 (pt) REVERT: P 288 MET cc_start: -0.1408 (ptt) cc_final: -0.1841 (tpp) REVERT: P 326 LEU cc_start: 0.3715 (tp) cc_final: 0.3426 (pp) REVERT: P 526 MET cc_start: -0.0590 (pmm) cc_final: -0.2020 (tpt) REVERT: P 577 MET cc_start: 0.1813 (mtp) cc_final: 0.0291 (tmm) REVERT: P 637 MET cc_start: 0.1013 (tmm) cc_final: 0.0591 (mtp) outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.1561 time to fit residues: 14.3955 Evaluate side-chains 53 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 429 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 180 GLN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 962 GLN ** P1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1294 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 7842 Z= 0.272 Angle : 0.969 29.965 10669 Z= 0.421 Chirality : 0.046 0.248 1266 Planarity : 0.007 0.094 1339 Dihedral : 5.886 56.098 1095 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.42 % Allowed : 13.49 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.51 (0.26), residues: 977 helix: -0.10 (0.24), residues: 442 sheet: 0.17 (0.51), residues: 89 loop : -2.22 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P1028 HIS 0.006 0.001 HIS P 822 PHE 0.021 0.002 PHE P1051 TYR 0.030 0.003 TYR P 173 ARG 0.006 0.001 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3150 (mt) cc_final: 0.2780 (pt) REVERT: P 275 LEU cc_start: 0.0482 (OUTLIER) cc_final: 0.0189 (mp) REVERT: P 577 MET cc_start: 0.2362 (mtp) cc_final: 0.0538 (tmm) REVERT: P 748 MET cc_start: 0.3902 (OUTLIER) cc_final: 0.3264 (ppp) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.1742 time to fit residues: 20.4896 Evaluate side-chains 70 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 748 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 962 GLN Chi-restraints excluded: chain P residue 1017 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 81 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1047 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1504 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7842 Z= 0.200 Angle : 0.899 30.869 10669 Z= 0.375 Chirality : 0.041 0.163 1266 Planarity : 0.005 0.043 1339 Dihedral : 5.490 54.330 1095 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.66 % Allowed : 17.16 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.44 (0.26), residues: 977 helix: 0.06 (0.24), residues: 447 sheet: 0.14 (0.54), residues: 82 loop : -2.28 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 583 HIS 0.002 0.001 HIS P 390 PHE 0.014 0.001 PHE P1051 TYR 0.020 0.002 TYR P 871 ARG 0.004 0.001 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 577 MET cc_start: 0.2478 (mtp) cc_final: 0.0619 (tmm) REVERT: P 837 PHE cc_start: 0.4987 (t80) cc_final: 0.4633 (p90) REVERT: P 964 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6450 (tp) REVERT: P 1091 VAL cc_start: 0.2767 (p) cc_final: 0.2407 (t) outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 0.1425 time to fit residues: 18.5927 Evaluate side-chains 75 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 971 THR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 overall best weight: 0.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1669 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7842 Z= 0.186 Angle : 0.892 30.354 10669 Z= 0.369 Chirality : 0.042 0.177 1266 Planarity : 0.005 0.043 1339 Dihedral : 5.033 51.002 1095 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.13 % Allowed : 17.63 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.17 (0.27), residues: 977 helix: 0.31 (0.25), residues: 447 sheet: 0.09 (0.54), residues: 82 loop : -2.14 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 175 HIS 0.003 0.001 HIS P 497 PHE 0.012 0.001 PHE P1051 TYR 0.018 0.002 TYR P 256 ARG 0.004 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 210 MET cc_start: 0.4913 (tmm) cc_final: 0.4618 (tmm) REVERT: P 577 MET cc_start: 0.2628 (mtp) cc_final: 0.0631 (tmm) REVERT: P 964 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7342 (tp) REVERT: P 1032 LEU cc_start: 0.3979 (OUTLIER) cc_final: 0.3739 (pp) REVERT: P 1091 VAL cc_start: 0.3366 (p) cc_final: 0.2997 (t) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1384 time to fit residues: 19.6244 Evaluate side-chains 81 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1032 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 18 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 44 optimal weight: 0.0470 chunk 7 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.1350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1595 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7842 Z= 0.154 Angle : 0.871 30.460 10669 Z= 0.354 Chirality : 0.041 0.152 1266 Planarity : 0.005 0.047 1339 Dihedral : 4.826 50.034 1095 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.13 % Allowed : 18.58 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.82 (0.27), residues: 977 helix: 0.64 (0.25), residues: 437 sheet: 0.11 (0.54), residues: 86 loop : -1.92 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 643 HIS 0.003 0.001 HIS P 836 PHE 0.011 0.001 PHE P 837 TYR 0.012 0.001 TYR P 952 ARG 0.002 0.000 ARG P 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.5312 (tmm) cc_final: 0.4776 (tmm) REVERT: P 326 LEU cc_start: 0.5305 (tp) cc_final: 0.3350 (mp) REVERT: P 526 MET cc_start: 0.1377 (mpp) cc_final: 0.1164 (pmm) REVERT: P 577 MET cc_start: 0.2538 (mtp) cc_final: 0.0595 (tmm) REVERT: P 964 LEU cc_start: 0.8024 (tt) cc_final: 0.7299 (tp) REVERT: P 1091 VAL cc_start: 0.3287 (p) cc_final: 0.2924 (t) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.1568 time to fit residues: 19.8807 Evaluate side-chains 74 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 HIS Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1044 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2328 moved from start: 0.8293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7842 Z= 0.278 Angle : 1.056 32.662 10669 Z= 0.464 Chirality : 0.048 0.268 1266 Planarity : 0.007 0.061 1339 Dihedral : 6.044 51.674 1095 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.37 % Allowed : 19.05 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.80 (0.26), residues: 977 helix: -0.29 (0.24), residues: 449 sheet: -0.11 (0.58), residues: 70 loop : -2.35 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 258 HIS 0.006 0.002 HIS P 836 PHE 0.023 0.002 PHE P1051 TYR 0.045 0.003 TYR P 871 ARG 0.008 0.001 ARG P 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: P 637 MET cc_start: -0.0225 (mtp) cc_final: -0.0824 (ttt) REVERT: P 748 MET cc_start: 0.4924 (ppp) cc_final: 0.3076 (ppp) REVERT: P 919 VAL cc_start: 0.2261 (OUTLIER) cc_final: 0.1410 (p) REVERT: P 940 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.4344 (t80) REVERT: P 952 TYR cc_start: 0.5229 (m-80) cc_final: 0.4923 (m-80) outliers start: 20 outliers final: 11 residues processed: 94 average time/residue: 0.1660 time to fit residues: 23.2137 Evaluate side-chains 80 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 261 LEU Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 919 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 971 THR Chi-restraints excluded: chain P residue 973 THR Chi-restraints excluded: chain P residue 1044 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2238 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7842 Z= 0.186 Angle : 0.927 30.210 10669 Z= 0.388 Chirality : 0.042 0.149 1266 Planarity : 0.005 0.048 1339 Dihedral : 5.499 50.108 1095 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.78 % Allowed : 21.54 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.19 (0.27), residues: 977 helix: 0.28 (0.24), residues: 442 sheet: -0.09 (0.63), residues: 62 loop : -1.98 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P1028 HIS 0.003 0.001 HIS P 198 PHE 0.010 0.001 PHE P 837 TYR 0.022 0.002 TYR P 871 ARG 0.004 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: P 105 VAL cc_start: 0.2197 (m) cc_final: 0.1697 (t) REVERT: P 257 TYR cc_start: 0.1268 (OUTLIER) cc_final: -0.1729 (m-80) REVERT: P 339 MET cc_start: 0.1975 (ptp) cc_final: 0.1702 (ptt) REVERT: P 637 MET cc_start: -0.0147 (mtp) cc_final: -0.0633 (ttt) REVERT: P 937 MET cc_start: 0.5311 (mmp) cc_final: 0.4331 (mmp) REVERT: P 940 TYR cc_start: 0.4537 (OUTLIER) cc_final: 0.4255 (t80) REVERT: P 952 TYR cc_start: 0.4869 (m-80) cc_final: 0.4558 (m-80) REVERT: P 1045 TYR cc_start: 0.1651 (m-80) cc_final: 0.0997 (m-80) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.1497 time to fit residues: 18.4778 Evaluate side-chains 74 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 282 SER Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1044 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P1047 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2632 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7842 Z= 0.245 Angle : 1.017 31.977 10669 Z= 0.445 Chirality : 0.046 0.179 1266 Planarity : 0.006 0.049 1339 Dihedral : 6.384 51.404 1095 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.78 % Allowed : 22.01 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.56 (0.27), residues: 977 helix: 0.01 (0.25), residues: 433 sheet: -0.38 (0.62), residues: 64 loop : -2.17 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP P1028 HIS 0.004 0.001 HIS P 772 PHE 0.012 0.002 PHE P 264 TYR 0.036 0.003 TYR P 871 ARG 0.005 0.001 ARG P 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: P 257 TYR cc_start: 0.2086 (OUTLIER) cc_final: -0.1135 (m-80) REVERT: P 339 MET cc_start: 0.2106 (ptp) cc_final: 0.1831 (ptt) REVERT: P 373 THR cc_start: 0.0588 (OUTLIER) cc_final: -0.0327 (m) REVERT: P 451 ARG cc_start: 0.2379 (tpt90) cc_final: 0.1818 (mmm160) REVERT: P 637 MET cc_start: -0.0146 (mtp) cc_final: -0.0619 (ttt) REVERT: P 748 MET cc_start: 0.5122 (ppp) cc_final: 0.3149 (ppp) REVERT: P 937 MET cc_start: 0.6126 (mmp) cc_final: 0.5347 (mmp) REVERT: P 940 TYR cc_start: 0.4194 (OUTLIER) cc_final: 0.2352 (t80) REVERT: P 952 TYR cc_start: 0.5045 (m-80) cc_final: 0.4722 (m-80) REVERT: P 1020 TYR cc_start: 0.2556 (t80) cc_final: 0.1369 (p90) REVERT: P 1133 MET cc_start: 0.4878 (ttt) cc_final: 0.4671 (mtp) outliers start: 15 outliers final: 9 residues processed: 91 average time/residue: 0.1684 time to fit residues: 22.4722 Evaluate side-chains 85 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 573 MET Chi-restraints excluded: chain P residue 908 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 20.0000 chunk 65 optimal weight: 0.3980 chunk 98 optimal weight: 0.4980 chunk 90 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2568 moved from start: 1.0273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7842 Z= 0.195 Angle : 0.964 31.020 10669 Z= 0.411 Chirality : 0.043 0.150 1266 Planarity : 0.005 0.048 1339 Dihedral : 6.022 50.411 1095 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.42 % Allowed : 22.84 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.32 (0.27), residues: 977 helix: 0.25 (0.25), residues: 437 sheet: -0.39 (0.62), residues: 66 loop : -2.09 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP P 175 HIS 0.007 0.001 HIS P 836 PHE 0.011 0.001 PHE P1056 TYR 0.023 0.002 TYR P 871 ARG 0.003 0.000 ARG P 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: P 226 LYS cc_start: 0.4321 (mmtt) cc_final: 0.3570 (pttm) REVERT: P 257 TYR cc_start: 0.1720 (OUTLIER) cc_final: -0.1194 (m-80) REVERT: P 339 MET cc_start: 0.2171 (ptp) cc_final: 0.1899 (ptt) REVERT: P 373 THR cc_start: 0.0592 (OUTLIER) cc_final: -0.0339 (m) REVERT: P 451 ARG cc_start: 0.2096 (tpt90) cc_final: 0.1769 (mmm160) REVERT: P 526 MET cc_start: 0.2111 (mpp) cc_final: 0.1218 (pmm) REVERT: P 637 MET cc_start: -0.0075 (mtp) cc_final: -0.0522 (ttt) REVERT: P 676 MET cc_start: -0.0257 (ttm) cc_final: -0.0557 (tpp) REVERT: P 748 MET cc_start: 0.5240 (ppp) cc_final: 0.3210 (ppp) REVERT: P 918 MET cc_start: 0.1985 (mpp) cc_final: 0.1384 (ppp) REVERT: P 937 MET cc_start: 0.6063 (mmp) cc_final: 0.5055 (mmp) REVERT: P 1046 GLU cc_start: 0.3784 (mp0) cc_final: 0.3558 (mp0) REVERT: P 1119 LEU cc_start: 0.3095 (tt) cc_final: 0.2559 (tp) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.1672 time to fit residues: 20.9525 Evaluate side-chains 86 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 257 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 495 CYS Chi-restraints excluded: chain P residue 551 LEU Chi-restraints excluded: chain P residue 908 SER Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 0.0050 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 772 HIS P1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.295712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.280128 restraints weight = 12176.948| |-----------------------------------------------------------------------------| r_work (start): 0.5058 rms_B_bonded: 1.91 r_work: 0.4989 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2827 moved from start: 1.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7842 Z= 0.209 Angle : 0.976 31.407 10669 Z= 0.420 Chirality : 0.044 0.156 1266 Planarity : 0.006 0.048 1339 Dihedral : 6.142 51.088 1095 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.18 % Allowed : 23.79 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.45 (0.27), residues: 977 helix: 0.19 (0.25), residues: 442 sheet: -0.22 (0.71), residues: 50 loop : -2.22 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 175 HIS 0.004 0.001 HIS P 836 PHE 0.014 0.001 PHE P1128 TYR 0.023 0.002 TYR P 952 ARG 0.003 0.000 ARG P 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.38 seconds wall clock time: 34 minutes 37.41 seconds (2077.41 seconds total)