Starting phenix.real_space_refine on Fri Feb 16 06:55:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9n_29872/02_2024/8g9n_29872_trim_updated.pdb" } resolution = 3.5 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 25 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 4675 2.51 5 N 1261 2.21 5 O 1432 1.98 5 H 7268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14695 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: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'DOC': 1} Classifications: {'DNA': 8, 'undetermined': 1} Link IDs: {'rna3p': 7, None: 1} Not linked: pdbres=" DG D 19 " pdbres="DOC D 20 " 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: 7.68, per 1000 atoms: 0.52 Number of scatterers: 14695 At special positions: 0 Unit cell: (106.47, 105.105, 96.915, 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 25 15.00 Mg 1 11.99 O 1432 8.00 N 1261 7.00 C 4675 6.00 H 7268 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: 14.75 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: 30 helices and 6 sheets defined 38.1% alpha, 15.3% beta 7 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 410 through 425 removed outlier: 3.807A pdb=" N VAL A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) 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 659 through 662 Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.661A pdb=" N ALA A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 725 through 731 removed outlier: 4.028A pdb=" N ARG A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 758 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.585A pdb=" N MET A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 797 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 906 through 925 Processing helix chain 'A' and resid 932 through 956 removed outlier: 4.028A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 Processing helix chain 'A' and resid 1011 through 1028 removed outlier: 4.481A 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 1187 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1213 through 1219 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: 3.592A pdb=" N SER A 497 " --> pdb=" O TRP A 345 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TRP A 366 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 348 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 516 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER A 379 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA A 518 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 389 Processing sheet with id= C, first strand: chain 'A' and resid 689 through 692 removed outlier: 5.935A pdb=" N VAL A 547 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE A 557 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 5.566A 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: 7.143A pdb=" N LYS A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1001 through 1005 removed outlier: 6.319A pdb=" N ASP A 859 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE A1036 " --> pdb=" O ASP A 859 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1131 through 1134 294 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 15.12 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: 7252 1.03 - 1.23: 32 1.23 - 1.42: 3142 1.42 - 1.61: 4419 1.61 - 1.81: 50 Bond restraints: 14895 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 20 " pdb=" C3' DOC D 20 " ideal model delta sigma weight residual 1.334 1.548 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C4' DGT A1501 " pdb=" O4' DGT A1501 " ideal model delta sigma weight residual 1.272 1.448 -0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" O4' DOC D 20 " pdb=" C1' DOC D 20 " ideal model delta sigma weight residual 1.268 1.437 -0.169 2.00e-02 2.50e+03 7.10e+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 14890 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.19: 433 107.19 - 114.02: 18124 114.02 - 120.84: 5064 120.84 - 127.67: 3291 127.67 - 134.49: 108 Bond angle restraints: 27020 Sorted by residual: angle pdb=" OP1 DOC D 20 " pdb=" P DOC D 20 " pdb=" OP2 DOC D 20 " ideal model delta sigma weight residual 109.57 119.93 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" PA DGT A1501 " pdb=" O3A DGT A1501 " pdb=" PB DGT A1501 " ideal model delta sigma weight residual 123.57 131.65 -8.08 3.00e+00 1.11e-01 7.25e+00 angle pdb=" PB DGT A1501 " pdb=" O3B DGT A1501 " pdb=" PG DGT A1501 " ideal model delta sigma weight residual 123.56 131.63 -8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" CA VAL A 558 " pdb=" C VAL A 558 " pdb=" N ALA A 559 " ideal model delta sigma weight residual 116.60 119.83 -3.23 1.45e+00 4.76e-01 4.97e+00 angle pdb=" C5' DGT A1501 " pdb=" O5' DGT A1501 " pdb=" PA DGT A1501 " ideal model delta sigma weight residual 118.41 124.16 -5.75 3.00e+00 1.11e-01 3.68e+00 ... (remaining 27015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.65: 6348 26.65 - 53.30: 479 53.30 - 79.94: 66 79.94 - 106.59: 6 106.59 - 133.24: 1 Dihedral angle restraints: 6900 sinusoidal: 3925 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 301.68 168.44 133.24 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA LEU A1148 " pdb=" C LEU A1148 " pdb=" N PRO A1149 " pdb=" CA PRO A1149 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 859 " pdb=" CB ASP A 859 " pdb=" CG ASP A 859 " pdb=" OD1 ASP A 859 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1036 0.069 - 0.138: 132 0.138 - 0.207: 4 0.207 - 0.276: 0 0.276 - 0.345: 1 Chirality restraints: 1173 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 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C4' DOC D 20 " pdb=" C5' DOC D 20 " pdb=" O4' DOC D 20 " pdb=" C3' DOC D 20 " both_signs ideal model delta sigma weight residual False -2.52 -2.70 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" C1' DOC D 20 " pdb=" O4' DOC D 20 " pdb=" C2' DOC D 20 " pdb=" N1 DOC D 20 " both_signs ideal model delta sigma weight residual False 2.33 2.50 -0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 1170 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 864 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 865 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 865 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 865 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 535 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 536 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1150 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C HIS A1150 " 0.020 2.00e-02 2.50e+03 pdb=" O HIS A1150 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL A1151 " -0.007 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1100 2.21 - 2.81: 30819 2.81 - 3.41: 38411 3.41 - 4.00: 51872 4.00 - 4.60: 79107 Nonbonded interactions: 201309 Sorted by model distance: nonbonded pdb=" H ASN A 549 " pdb=" O GLN A 554 " model vdw 1.615 1.850 nonbonded pdb=" OE1 GLU A 384 " pdb=" H GLU A 384 " model vdw 1.640 1.850 nonbonded pdb=" OE2 GLU A 454 " pdb=" HE ARG A 456 " model vdw 1.643 1.850 nonbonded pdb=" OG SER A1097 " pdb="HE21 GLN A1099 " model vdw 1.652 1.850 nonbonded pdb=" O GLN A1205 " pdb=" HG SER A1209 " model vdw 1.678 1.850 ... (remaining 201304 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.240 Extract box with map and model: 3.720 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 59.260 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 7627 Z= 0.434 Angle : 0.508 10.355 10429 Z= 0.261 Chirality : 0.043 0.345 1173 Planarity : 0.003 0.031 1254 Dihedral : 19.006 133.240 2921 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 21.91 % Favored : 78.09 % 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: 0.89 (0.30), residues: 862 helix: 1.84 (0.29), residues: 341 sheet: 0.73 (0.41), residues: 140 loop : -0.60 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.002 0.000 HIS A 582 PHE 0.009 0.001 PHE A 583 TYR 0.008 0.001 TYR A1206 ARG 0.003 0.000 ARG A1187 *********************** 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 123 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.183 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 990 MET cc_start: 0.8473 (ttm) cc_final: 0.8129 (mtp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4808 time to fit residues: 77.5534 Evaluate side-chains 68 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS A 799 ASN A 861 ASN A1007 ASN A1099 GLN A1118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7627 Z= 0.254 Angle : 0.517 4.350 10429 Z= 0.277 Chirality : 0.041 0.142 1173 Planarity : 0.003 0.027 1254 Dihedral : 14.257 122.832 1180 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.29 % Allowed : 23.07 % Favored : 75.64 % 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: 0.88 (0.29), residues: 862 helix: 1.81 (0.28), residues: 350 sheet: 0.68 (0.42), residues: 137 loop : -0.62 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1156 HIS 0.003 0.001 HIS A 582 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A 732 ARG 0.008 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 74 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 1.298 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8234 (t0) cc_final: 0.7915 (t0) REVERT: A 597 ASP cc_start: 0.8277 (t70) cc_final: 0.8032 (t0) REVERT: A 756 MET cc_start: 0.7755 (ttt) cc_final: 0.7370 (ttm) REVERT: A 939 ASP cc_start: 0.8165 (t0) cc_final: 0.7905 (t0) REVERT: A 990 MET cc_start: 0.8540 (ttm) cc_final: 0.8216 (mtp) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.4774 time to fit residues: 46.9767 Evaluate side-chains 63 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 HIS ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7627 Z= 0.270 Angle : 0.517 4.330 10429 Z= 0.277 Chirality : 0.041 0.143 1173 Planarity : 0.003 0.027 1254 Dihedral : 14.013 115.844 1180 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.06 % Allowed : 22.55 % Favored : 75.39 % 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: 0.87 (0.29), residues: 862 helix: 1.85 (0.28), residues: 349 sheet: 0.53 (0.42), residues: 139 loop : -0.61 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.003 0.001 HIS A 582 PHE 0.011 0.001 PHE A 487 TYR 0.011 0.001 TYR A 640 ARG 0.004 0.000 ARG A 682 *********************** 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 73 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 1.172 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.8279 (t70) cc_final: 0.8013 (t0) REVERT: A 781 MET cc_start: 0.9131 (ttp) cc_final: 0.8862 (ttm) REVERT: A 990 MET cc_start: 0.8565 (ttm) cc_final: 0.8249 (mtp) outliers start: 16 outliers final: 13 residues processed: 71 average time/residue: 0.4126 time to fit residues: 40.9151 Evaluate side-chains 65 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1157 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7627 Z= 0.179 Angle : 0.479 4.705 10429 Z= 0.256 Chirality : 0.041 0.138 1173 Planarity : 0.003 0.029 1254 Dihedral : 13.809 105.532 1180 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.80 % Allowed : 23.32 % Favored : 74.87 % 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: 1.13 (0.30), residues: 862 helix: 2.17 (0.29), residues: 343 sheet: 0.49 (0.41), residues: 144 loop : -0.48 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.002 0.001 HIS A1150 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A1206 ARG 0.002 0.000 ARG A1020 *********************** 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 69 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.200 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.8271 (t70) cc_final: 0.8010 (t0) REVERT: A 781 MET cc_start: 0.9116 (ttp) cc_final: 0.8811 (ttm) REVERT: A 990 MET cc_start: 0.8529 (ttm) cc_final: 0.8202 (mtp) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.4275 time to fit residues: 39.4427 Evaluate side-chains 64 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7627 Z= 0.332 Angle : 0.555 5.131 10429 Z= 0.298 Chirality : 0.042 0.139 1173 Planarity : 0.003 0.034 1254 Dihedral : 13.620 87.647 1180 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.93 % Allowed : 23.45 % Favored : 74.61 % 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: 0.64 (0.29), residues: 862 helix: 1.68 (0.28), residues: 349 sheet: 0.20 (0.40), residues: 146 loop : -0.67 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1156 HIS 0.003 0.001 HIS A 582 PHE 0.012 0.001 PHE A 487 TYR 0.008 0.001 TYR A 838 ARG 0.002 0.000 ARG A 778 *********************** 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 69 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.266 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8412 (t0) cc_final: 0.8100 (t0) REVERT: A 597 ASP cc_start: 0.8317 (t70) cc_final: 0.8051 (t0) REVERT: A 776 MET cc_start: 0.8088 (ttm) cc_final: 0.7883 (ttm) REVERT: A 781 MET cc_start: 0.9156 (ttp) cc_final: 0.8881 (ttm) REVERT: A 990 MET cc_start: 0.8605 (ttm) cc_final: 0.8330 (mtp) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.4028 time to fit residues: 37.8976 Evaluate side-chains 60 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7627 Z= 0.174 Angle : 0.486 5.631 10429 Z= 0.259 Chirality : 0.041 0.136 1173 Planarity : 0.003 0.048 1254 Dihedral : 13.444 75.212 1180 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.32 % Allowed : 23.32 % Favored : 74.36 % 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: 1.02 (0.30), residues: 862 helix: 2.10 (0.29), residues: 348 sheet: 0.25 (0.40), residues: 145 loop : -0.51 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A1206 ARG 0.001 0.000 ARG A1020 *********************** 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 71 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 1.219 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 revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.8344 (t70) cc_final: 0.8093 (t0) REVERT: A 781 MET cc_start: 0.9107 (ttp) cc_final: 0.8836 (ttm) REVERT: A 990 MET cc_start: 0.8546 (ttm) cc_final: 0.8204 (mtp) outliers start: 18 outliers final: 16 residues processed: 67 average time/residue: 0.3996 time to fit residues: 37.9490 Evaluate side-chains 66 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7627 Z= 0.213 Angle : 0.501 4.923 10429 Z= 0.267 Chirality : 0.041 0.137 1173 Planarity : 0.003 0.053 1254 Dihedral : 13.322 74.354 1180 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.19 % Allowed : 23.71 % Favored : 74.10 % 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: 1.05 (0.30), residues: 862 helix: 2.14 (0.29), residues: 348 sheet: 0.25 (0.40), residues: 145 loop : -0.50 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A 953 ARG 0.001 0.000 ARG A 682 *********************** 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 69 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 1.284 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8345 (t0) cc_final: 0.8032 (t0) REVERT: A 597 ASP cc_start: 0.8355 (t70) cc_final: 0.8106 (t0) REVERT: A 781 MET cc_start: 0.9107 (ttp) cc_final: 0.8841 (ttm) REVERT: A 990 MET cc_start: 0.8498 (ttm) cc_final: 0.8247 (mtp) outliers start: 17 outliers final: 16 residues processed: 66 average time/residue: 0.4189 time to fit residues: 38.7633 Evaluate side-chains 64 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1176 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7627 Z= 0.339 Angle : 0.553 5.245 10429 Z= 0.300 Chirality : 0.042 0.141 1173 Planarity : 0.004 0.050 1254 Dihedral : 13.311 77.466 1180 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.45 % Allowed : 23.58 % Favored : 73.97 % 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: 0.59 (0.29), residues: 862 helix: 1.68 (0.28), residues: 348 sheet: 0.08 (0.40), residues: 149 loop : -0.71 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1156 HIS 0.004 0.001 HIS A 582 PHE 0.010 0.001 PHE A 487 TYR 0.009 0.001 TYR A 953 ARG 0.002 0.000 ARG A 918 *********************** 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 70 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 1.218 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 revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.7932 (t70) cc_final: 0.7706 (t0) REVERT: A 781 MET cc_start: 0.9158 (ttp) cc_final: 0.8895 (ttm) REVERT: A 990 MET cc_start: 0.8598 (ttm) cc_final: 0.8333 (mtp) outliers start: 19 outliers final: 17 residues processed: 66 average time/residue: 0.4056 time to fit residues: 37.5935 Evaluate side-chains 64 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7627 Z= 0.198 Angle : 0.505 5.935 10429 Z= 0.270 Chirality : 0.040 0.136 1173 Planarity : 0.003 0.060 1254 Dihedral : 13.206 77.752 1180 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.45 % Allowed : 23.58 % Favored : 73.97 % 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: 0.90 (0.30), residues: 862 helix: 2.03 (0.28), residues: 347 sheet: 0.25 (0.40), residues: 147 loop : -0.63 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.003 0.001 HIS A1150 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A 953 ARG 0.003 0.000 ARG A 682 *********************** 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 70 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 1.222 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.7983 (t70) cc_final: 0.7749 (t0) REVERT: A 682 ARG cc_start: 0.8046 (tpt90) cc_final: 0.7678 (tpt170) REVERT: A 781 MET cc_start: 0.9117 (ttp) cc_final: 0.8853 (ttm) REVERT: A 990 MET cc_start: 0.8505 (ttm) cc_final: 0.8266 (mtp) outliers start: 19 outliers final: 17 residues processed: 66 average time/residue: 0.4168 time to fit residues: 38.8084 Evaluate side-chains 68 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1176 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7627 Z= 0.169 Angle : 0.490 6.688 10429 Z= 0.261 Chirality : 0.040 0.136 1173 Planarity : 0.003 0.053 1254 Dihedral : 13.072 77.618 1180 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.06 % Allowed : 23.84 % Favored : 74.10 % 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: 1.19 (0.30), residues: 862 helix: 2.35 (0.29), residues: 348 sheet: 0.25 (0.40), residues: 145 loop : -0.49 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 366 HIS 0.002 0.001 HIS A 565 PHE 0.005 0.001 PHE A 679 TYR 0.007 0.001 TYR A1206 ARG 0.003 0.000 ARG A 682 ********************** 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 70 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 1.215 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8329 (t0) cc_final: 0.8020 (t0) REVERT: A 597 ASP cc_start: 0.7937 (t70) cc_final: 0.7698 (t0) REVERT: A 682 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7898 (tpt170) REVERT: A 781 MET cc_start: 0.9109 (ttp) cc_final: 0.8849 (ttm) REVERT: A 990 MET cc_start: 0.8446 (ttm) cc_final: 0.8208 (mtp) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.4041 time to fit residues: 38.7456 Evaluate side-chains 63 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1176 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.055006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.043818 restraints weight = 106121.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046090 restraints weight = 43506.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047542 restraints weight = 25127.764| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7627 Z= 0.227 Angle : 0.507 6.638 10429 Z= 0.271 Chirality : 0.040 0.135 1173 Planarity : 0.003 0.049 1254 Dihedral : 13.049 78.323 1180 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.80 % Allowed : 23.97 % Favored : 74.23 % 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: 1.00 (0.30), residues: 862 helix: 2.12 (0.28), residues: 354 sheet: 0.17 (0.40), residues: 145 loop : -0.57 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1156 HIS 0.004 0.001 HIS A1150 PHE 0.007 0.001 PHE A 487 TYR 0.008 0.001 TYR A 953 ARG 0.003 0.000 ARG A 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.93 seconds wall clock time: 62 minutes 10.89 seconds (3730.89 seconds total)