Starting phenix.real_space_refine on Sat Mar 16 13:00:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucu_42140/03_2024/8ucu_42140_trim_updated.pdb" } resolution = 2.85 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= 0.002 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 P 27 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 4694 2.51 5 N 1269 2.21 5 O 1444 1.98 5 H 7290 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 416": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 13976 Classifications: {'peptide': 868} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 822} Chain breaks: 2 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 443 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 307 Unusual residues: {'DOC': 1} Classifications: {'DNA': 9, 'undetermined': 1} Link IDs: {'rna3p': 8, None: 1} Not linked: pdbres=" DG D 28 " pdbres="DOC D 29 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.81, per 1000 atoms: 0.46 Number of scatterers: 14758 At special positions: 0 Unit cell: (114.8, 95.12, 102.773, 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 33 16.00 P 27 15.00 Mg 1 11.99 O 1444 8.00 N 1269 7.00 C 4694 6.00 H 7290 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 11.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 6 sheets defined 38.7% alpha, 15.9% beta 9 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 7.87 Creating SS restraints... Processing helix chain 'A' and resid 410 through 419 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 735 through 759 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 785 through 799 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 926 Processing helix chain 'A' and resid 932 through 957 removed outlier: 4.005A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 4.276A pdb=" N SER A1028 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1082 through 1096 Processing helix chain 'A' and resid 1101 through 1121 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1210 Processing helix chain 'A' and resid 1213 through 1222 Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1228 through 1234 Processing sheet with id= A, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.768A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 372 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LYS A 381 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 520 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 390 removed outlier: 3.500A pdb=" N LEU A 389 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 6.122A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN A 549 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN A 555 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL A 558 " --> pdb=" O SER A 587 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 849 through 851 removed outlier: 7.069A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1034 through 1040 removed outlier: 6.837A pdb=" N LEU A 857 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A1039 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 855 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR A 996 " --> pdb=" O MET A1003 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A1005 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 994 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1133 297 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 6.10 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7274 1.03 - 1.23: 27 1.23 - 1.42: 3175 1.42 - 1.61: 4437 1.61 - 1.81: 50 Bond restraints: 14963 Sorted by residual: bond pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " ideal model delta sigma weight residual 1.284 1.542 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C4' DOC D 29 " pdb=" C3' DOC D 29 " ideal model delta sigma weight residual 1.334 1.547 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.447 -0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" O4' DOC D 29 " pdb=" C1' DOC D 29 " ideal model delta sigma weight residual 1.268 1.439 -0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C4 DGT A1501 " pdb=" N3 DGT A1501 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.00e-02 2.50e+03 7.01e+01 ... (remaining 14958 not shown) Histogram of bond angle deviations from ideal: 100.20 - 107.03: 412 107.03 - 113.86: 18123 113.86 - 120.69: 4993 120.69 - 127.53: 3498 127.53 - 134.36: 117 Bond angle restraints: 27143 Sorted by residual: angle pdb=" OP1 DOC D 29 " pdb=" P DOC D 29 " pdb=" OP2 DOC D 29 " ideal model delta sigma weight residual 109.57 120.05 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" PA DGT A1501 " pdb=" O3A DGT A1501 " pdb=" PB DGT A1501 " ideal model delta sigma weight residual 123.57 132.49 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" PB DGT A1501 " pdb=" O3B DGT A1501 " pdb=" PG DGT A1501 " ideal model delta sigma weight residual 123.56 131.48 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" C3' DA D 27 " pdb=" C2' DA D 27 " pdb=" C1' DA D 27 " ideal model delta sigma weight residual 101.60 104.56 -2.96 1.50e+00 4.44e-01 3.88e+00 angle pdb=" C2' DGT A1501 " pdb=" C3' DGT A1501 " pdb=" C4' DGT A1501 " ideal model delta sigma weight residual 105.71 100.20 5.51 3.00e+00 1.11e-01 3.38e+00 ... (remaining 27138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.78: 6372 25.78 - 51.57: 454 51.57 - 77.35: 86 77.35 - 103.13: 9 103.13 - 128.91: 1 Dihedral angle restraints: 6922 sinusoidal: 3947 harmonic: 2975 Sorted by residual: dihedral pdb=" O1B DGT A1501 " pdb=" O3B DGT A1501 " pdb=" PB DGT A1501 " pdb=" PG DGT A1501 " ideal model delta sinusoidal sigma weight residual 301.68 172.77 128.91 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CA VAL A 656 " pdb=" C VAL A 656 " pdb=" N PRO A 657 " pdb=" CA PRO A 657 " ideal model delta harmonic sigma weight residual 180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB GLU A 368 " pdb=" CG GLU A 368 " pdb=" CD GLU A 368 " pdb=" OE1 GLU A 368 " ideal model delta sinusoidal sigma weight residual 0.00 -86.49 86.49 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 6919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1050 0.068 - 0.137: 127 0.137 - 0.205: 3 0.205 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 1181 Sorted by residual: chirality pdb=" C3' DGT A1501 " pdb=" C2' DGT A1501 " pdb=" C4' DGT A1501 " pdb=" O3' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.42 -2.77 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C4' DOC D 29 " pdb=" C5' DOC D 29 " pdb=" O4' DOC D 29 " pdb=" C3' DOC D 29 " both_signs ideal model delta sigma weight residual False -2.52 -2.69 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" C4' DGT A1501 " pdb=" C3' DGT A1501 " pdb=" C5' DGT A1501 " pdb=" O4' DGT A1501 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1178 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1152 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C HIS A1152 " -0.022 2.00e-02 2.50e+03 pdb=" O HIS A1152 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A1153 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 907 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 908 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 864 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 865 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 865 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 865 " -0.017 5.00e-02 4.00e+02 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 2115 2.26 - 2.85: 33272 2.85 - 3.43: 37013 3.43 - 4.02: 53742 4.02 - 4.60: 80279 Nonbonded interactions: 206421 Sorted by model distance: nonbonded pdb=" OD1 ASP A 351 " pdb=" H SER A 354 " model vdw 1.680 1.850 nonbonded pdb=" O LYS A 847 " pdb=" HH TYR A 851 " model vdw 1.699 1.850 nonbonded pdb=" HG SER A 375 " pdb=" OD2 ASP A 630 " model vdw 1.703 1.850 nonbonded pdb=" O ALA A 765 " pdb=" HG1 THR A 769 " model vdw 1.717 1.850 nonbonded pdb=" H GLN A1177 " pdb=" O SER A1201 " model vdw 1.722 1.850 ... (remaining 206416 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: 1.190 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: 0.220 Extract box with map and model: 6.300 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 54.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.009 0.258 7673 Z= 0.419 Angle : 0.488 10.475 10500 Z= 0.245 Chirality : 0.044 0.341 1181 Planarity : 0.003 0.030 1256 Dihedral : 18.734 128.913 2941 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 17.91 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.77 (0.30), residues: 862 helix: 2.07 (0.28), residues: 357 sheet: 1.28 (0.44), residues: 144 loop : 0.31 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 345 HIS 0.003 0.001 HIS A1152 PHE 0.007 0.001 PHE A 583 TYR 0.009 0.001 TYR A 425 ARG 0.002 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 75 average time/residue: 3.4052 time to fit residues: 267.6682 Evaluate side-chains 34 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 770 ASN A 861 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7673 Z= 0.334 Angle : 0.538 4.987 10500 Z= 0.281 Chirality : 0.042 0.140 1181 Planarity : 0.003 0.042 1256 Dihedral : 14.847 128.645 1203 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.39 % Allowed : 20.49 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.68 (0.29), residues: 862 helix: 1.97 (0.28), residues: 365 sheet: 1.11 (0.43), residues: 142 loop : 0.30 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.004 0.001 HIS A1152 PHE 0.008 0.001 PHE A 362 TYR 0.009 0.001 TYR A 871 ARG 0.007 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 3.2199 time to fit residues: 115.9653 Evaluate side-chains 32 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7673 Z= 0.228 Angle : 0.488 4.722 10500 Z= 0.254 Chirality : 0.041 0.138 1181 Planarity : 0.003 0.031 1256 Dihedral : 14.377 114.197 1200 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.64 % Allowed : 19.85 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.77 (0.29), residues: 862 helix: 2.05 (0.28), residues: 360 sheet: 1.11 (0.44), residues: 137 loop : 0.41 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.008 0.001 PHE A1242 TYR 0.008 0.001 TYR A 953 ARG 0.002 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 3.0241 time to fit residues: 115.6239 Evaluate side-chains 31 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7673 Z= 0.289 Angle : 0.499 5.880 10500 Z= 0.260 Chirality : 0.042 0.140 1181 Planarity : 0.003 0.032 1256 Dihedral : 14.282 113.005 1200 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.42 % Allowed : 18.30 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.75 (0.30), residues: 862 helix: 2.10 (0.28), residues: 360 sheet: 0.98 (0.43), residues: 137 loop : 0.38 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.007 0.001 PHE A 362 TYR 0.009 0.001 TYR A 871 ARG 0.002 0.000 ARG A 977 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 41 average time/residue: 2.6523 time to fit residues: 116.1282 Evaluate side-chains 33 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.8532 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7673 Z= 0.255 Angle : 0.484 6.096 10500 Z= 0.252 Chirality : 0.041 0.141 1181 Planarity : 0.003 0.034 1256 Dihedral : 14.118 105.219 1200 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.16 % Allowed : 18.81 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.84 (0.30), residues: 862 helix: 2.16 (0.28), residues: 360 sheet: 1.00 (0.43), residues: 137 loop : 0.45 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 362 TYR 0.009 0.001 TYR A 871 ARG 0.002 0.000 ARG A1020 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8519 (t0) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 2.6325 time to fit residues: 110.1250 Evaluate side-chains 36 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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: 0.8531 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7673 Z= 0.233 Angle : 0.482 8.086 10500 Z= 0.249 Chirality : 0.041 0.139 1181 Planarity : 0.003 0.035 1256 Dihedral : 14.011 101.090 1200 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.16 % Allowed : 19.20 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.92 (0.30), residues: 862 helix: 2.22 (0.28), residues: 361 sheet: 1.08 (0.44), residues: 136 loop : 0.48 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 362 TYR 0.009 0.001 TYR A 953 ARG 0.001 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 2.6532 time to fit residues: 113.4984 Evaluate side-chains 35 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8524 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7673 Z= 0.193 Angle : 0.470 4.512 10500 Z= 0.244 Chirality : 0.041 0.139 1181 Planarity : 0.003 0.035 1256 Dihedral : 13.890 95.559 1200 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 18.81 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.02 (0.30), residues: 862 helix: 2.30 (0.28), residues: 361 sheet: 1.12 (0.44), residues: 136 loop : 0.54 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.001 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 2.6118 time to fit residues: 117.3083 Evaluate side-chains 38 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8530 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7673 Z= 0.213 Angle : 0.475 4.486 10500 Z= 0.247 Chirality : 0.041 0.148 1181 Planarity : 0.003 0.036 1256 Dihedral : 13.795 91.197 1200 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.16 % Allowed : 19.07 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.02 (0.30), residues: 862 helix: 2.36 (0.28), residues: 360 sheet: 1.06 (0.44), residues: 135 loop : 0.52 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 362 TYR 0.009 0.001 TYR A 953 ARG 0.001 0.000 ARG A1187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 2.5170 time to fit residues: 108.1620 Evaluate side-chains 36 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.8537 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7673 Z= 0.238 Angle : 0.482 5.700 10500 Z= 0.251 Chirality : 0.041 0.140 1181 Planarity : 0.003 0.035 1256 Dihedral : 13.728 85.713 1200 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.90 % Allowed : 19.46 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.01 (0.30), residues: 862 helix: 2.34 (0.28), residues: 362 sheet: 1.01 (0.44), residues: 135 loop : 0.54 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 362 TYR 0.009 0.001 TYR A 598 ARG 0.001 0.000 ARG A 977 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 2.7517 time to fit residues: 112.0014 Evaluate side-chains 36 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8534 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7673 Z= 0.218 Angle : 0.482 8.126 10500 Z= 0.251 Chirality : 0.041 0.140 1181 Planarity : 0.003 0.036 1256 Dihedral : 13.689 81.890 1200 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.90 % Allowed : 19.20 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.05 (0.30), residues: 862 helix: 2.37 (0.28), residues: 362 sheet: 1.02 (0.43), residues: 135 loop : 0.56 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 583 TYR 0.008 0.001 TYR A 953 ARG 0.001 0.000 ARG A1187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 2.7433 time to fit residues: 108.4221 Evaluate side-chains 37 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 788 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 982 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.040786 restraints weight = 86585.550| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.34 r_work: 0.2708 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7673 Z= 0.163 Angle : 0.466 7.385 10500 Z= 0.243 Chirality : 0.041 0.138 1181 Planarity : 0.003 0.036 1256 Dihedral : 13.587 76.000 1200 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.64 % Allowed : 19.33 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.19 (0.30), residues: 862 helix: 2.53 (0.28), residues: 359 sheet: 1.12 (0.44), residues: 136 loop : 0.59 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A1152 PHE 0.006 0.001 PHE A 583 TYR 0.009 0.001 TYR A 953 ARG 0.001 0.000 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4373.48 seconds wall clock time: 77 minutes 14.95 seconds (4634.95 seconds total)