Starting phenix.real_space_refine on Sun Mar 10 16:26:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctj_26992/03_2024/8ctj_26992_updated.pdb" } resolution = 4.74 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2202 2.51 5 N 529 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3312 Unusual residues: {'PEE': 1} Classifications: {'peptide': 401, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 390, None: 1} Not linked: pdbres="LEU A 474 " pdbres="PEE A 601 " Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 2.33, per 1000 atoms: 0.70 Number of scatterers: 3312 At special positions: 0 Unit cell: (55.75, 57.98, 105.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 562 8.00 N 529 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 709.1 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 56.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.651A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU A 102 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 109 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.729A pdb=" N PHE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 221 through 250 Proline residue: A 225 - end of helix removed outlier: 3.618A pdb=" N ILE A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 291 through 317 Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.554A pdb=" N MET A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 392 removed outlier: 4.074A pdb=" N PHE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 395 through 427 removed outlier: 3.747A pdb=" N ARG A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.323A pdb=" N GLN A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 470 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 59 195 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 977 1.34 - 1.47: 929 1.47 - 1.60: 1461 1.60 - 1.73: 1 1.73 - 1.86: 30 Bond restraints: 3398 Sorted by residual: bond pdb=" O4P PEE A 601 " pdb=" P PEE A 601 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 1.531 1.577 -0.047 3.12e-02 1.03e+03 2.25e+00 bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.855 -0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" C2 PEE A 601 " pdb=" C3 PEE A 601 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 3393 not shown) Histogram of bond angle deviations from ideal: 90.91 - 99.55: 3 99.55 - 108.20: 143 108.20 - 116.84: 2156 116.84 - 125.48: 2226 125.48 - 134.13: 75 Bond angle restraints: 4603 Sorted by residual: angle pdb=" O1P PEE A 601 " pdb=" P PEE A 601 " pdb=" O2P PEE A 601 " ideal model delta sigma weight residual 119.43 133.35 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 110.44 106.16 4.28 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CA TRP A 252 " pdb=" CB TRP A 252 " pdb=" CG TRP A 252 " ideal model delta sigma weight residual 113.60 120.05 -6.45 1.90e+00 2.77e-01 1.15e+01 angle pdb=" CA MET A 231 " pdb=" CB MET A 231 " pdb=" CG MET A 231 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 1924 29.18 - 58.35: 50 58.35 - 87.53: 6 87.53 - 116.71: 0 116.71 - 145.89: 2 Dihedral angle restraints: 1982 sinusoidal: 805 harmonic: 1177 Sorted by residual: dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 431 " pdb=" CB CYS A 431 " ideal model delta sinusoidal sigma weight residual 93.00 144.73 -51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" O2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual -59.96 85.93 -145.89 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " pdb=" O3P PEE A 601 " ideal model delta sinusoidal sigma weight residual 62.73 -156.57 -140.70 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 1979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 459 0.077 - 0.155: 54 0.155 - 0.232: 6 0.232 - 0.309: 0 0.309 - 0.387: 1 Chirality restraints: 520 Sorted by residual: chirality pdb=" C2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C3 PEE A 601 " pdb=" O2 PEE A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 517 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 371 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP A 371 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 371 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 371 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 135 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN A 135 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 404 " -0.010 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A 404 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 404 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 404 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 404 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 404 " 0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 539 2.77 - 3.30: 3286 3.30 - 3.83: 5411 3.83 - 4.37: 5971 4.37 - 4.90: 10264 Nonbonded interactions: 25471 Sorted by model distance: nonbonded pdb=" O TYR A 340 " pdb=" OG SER A 344 " model vdw 2.233 2.440 nonbonded pdb=" OG SER A 77 " pdb=" O SER A 191 " model vdw 2.233 2.440 nonbonded pdb=" O ILE A 419 " pdb=" OG1 THR A 423 " model vdw 2.276 2.440 nonbonded pdb=" O ASN A 200 " pdb=" OG SER A 203 " model vdw 2.312 2.440 nonbonded pdb=" O SER A 399 " pdb=" ND1 HIS A 403 " model vdw 2.381 2.520 ... (remaining 25466 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 3398 Z= 0.316 Angle : 0.917 13.923 4603 Z= 0.487 Chirality : 0.051 0.387 520 Planarity : 0.006 0.052 551 Dihedral : 14.667 145.887 1214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.41), residues: 395 helix: 0.26 (0.32), residues: 229 sheet: -1.55 (0.73), residues: 47 loop : -1.24 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 244 HIS 0.001 0.000 HIS A 43 PHE 0.035 0.003 PHE A 379 TYR 0.018 0.003 TYR A 277 ARG 0.010 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.1993 (mtt) cc_final: 0.1692 (mtt) REVERT: A 227 MET cc_start: 0.8191 (tmm) cc_final: 0.7913 (tmm) REVERT: A 270 MET cc_start: 0.4612 (mmt) cc_final: 0.3946 (mmt) REVERT: A 386 MET cc_start: 0.8365 (tpp) cc_final: 0.7971 (tpp) REVERT: A 438 LEU cc_start: 0.6769 (mp) cc_final: 0.6373 (tp) REVERT: A 440 VAL cc_start: 0.9073 (t) cc_final: 0.8753 (p) REVERT: A 453 LEU cc_start: 0.8336 (mt) cc_final: 0.8123 (mt) REVERT: A 457 MET cc_start: 0.5495 (mtm) cc_final: 0.4779 (ptp) REVERT: A 467 GLN cc_start: 0.8176 (tt0) cc_final: 0.7943 (tt0) REVERT: A 468 ARG cc_start: 0.8817 (mtm180) cc_final: 0.7808 (mmm160) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1852 time to fit residues: 23.8065 Evaluate side-chains 87 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 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 91 ASN A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3398 Z= 0.228 Angle : 0.694 11.043 4603 Z= 0.356 Chirality : 0.043 0.206 520 Planarity : 0.006 0.049 551 Dihedral : 11.570 134.083 453 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.42), residues: 395 helix: 1.07 (0.34), residues: 224 sheet: -1.25 (0.76), residues: 47 loop : -0.91 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 252 HIS 0.007 0.002 HIS A 43 PHE 0.024 0.003 PHE A 276 TYR 0.010 0.002 TYR A 401 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.5859 (m-80) cc_final: 0.5603 (m-80) REVERT: A 91 ASN cc_start: 0.7178 (m-40) cc_final: 0.6603 (p0) REVERT: A 206 PHE cc_start: 0.7296 (m-80) cc_final: 0.7082 (m-80) REVERT: A 227 MET cc_start: 0.8427 (tmm) cc_final: 0.8015 (tmm) REVERT: A 346 MET cc_start: 0.2241 (mmt) cc_final: 0.1779 (mmt) REVERT: A 386 MET cc_start: 0.8209 (tpp) cc_final: 0.7861 (tpp) REVERT: A 387 LYS cc_start: 0.8964 (tptt) cc_final: 0.8626 (ttmt) REVERT: A 438 LEU cc_start: 0.7684 (mp) cc_final: 0.7135 (tp) REVERT: A 453 LEU cc_start: 0.8324 (mt) cc_final: 0.8053 (mt) REVERT: A 457 MET cc_start: 0.6134 (mtm) cc_final: 0.5555 (ptp) REVERT: A 467 GLN cc_start: 0.8229 (tt0) cc_final: 0.7982 (tt0) REVERT: A 468 ARG cc_start: 0.9006 (mtm180) cc_final: 0.7837 (mmm160) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1886 time to fit residues: 22.9478 Evaluate side-chains 81 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 187 HIS A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3398 Z= 0.167 Angle : 0.583 10.667 4603 Z= 0.299 Chirality : 0.040 0.147 520 Planarity : 0.005 0.043 551 Dihedral : 11.043 125.945 453 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.43), residues: 395 helix: 1.32 (0.35), residues: 215 sheet: -0.81 (0.69), residues: 56 loop : -0.80 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.007 0.002 HIS A 187 PHE 0.012 0.002 PHE A 404 TYR 0.012 0.001 TYR A 94 ARG 0.008 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8067 (mt) cc_final: 0.7160 (mt) REVERT: A 206 PHE cc_start: 0.7340 (m-80) cc_final: 0.7046 (m-80) REVERT: A 227 MET cc_start: 0.8576 (tmm) cc_final: 0.8093 (tmm) REVERT: A 298 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6842 (tp30) REVERT: A 386 MET cc_start: 0.8322 (tpp) cc_final: 0.7826 (tpp) REVERT: A 387 LYS cc_start: 0.8923 (tptt) cc_final: 0.8543 (tttp) REVERT: A 438 LEU cc_start: 0.8113 (mp) cc_final: 0.7459 (tp) REVERT: A 453 LEU cc_start: 0.8276 (mt) cc_final: 0.7955 (mt) REVERT: A 457 MET cc_start: 0.5832 (mtm) cc_final: 0.5294 (ptp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1575 time to fit residues: 18.7565 Evaluate side-chains 81 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN A 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.8226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 3398 Z= 0.331 Angle : 0.876 14.251 4603 Z= 0.454 Chirality : 0.049 0.246 520 Planarity : 0.006 0.044 551 Dihedral : 11.480 120.125 453 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.41), residues: 395 helix: 0.56 (0.34), residues: 212 sheet: -1.19 (0.67), residues: 54 loop : -1.36 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 252 HIS 0.008 0.003 HIS A 43 PHE 0.027 0.003 PHE A 260 TYR 0.023 0.003 TYR A 94 ARG 0.009 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.6398 (m-10) cc_final: 0.5592 (m-80) REVERT: A 227 MET cc_start: 0.8654 (tmm) cc_final: 0.7944 (tmm) REVERT: A 259 GLN cc_start: 0.8158 (mp10) cc_final: 0.7826 (mp10) REVERT: A 270 MET cc_start: 0.5610 (mmp) cc_final: 0.5135 (mmp) REVERT: A 298 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7088 (tp30) REVERT: A 346 MET cc_start: 0.2183 (mmt) cc_final: 0.1888 (mmt) REVERT: A 386 MET cc_start: 0.8715 (tpp) cc_final: 0.8225 (tpp) REVERT: A 387 LYS cc_start: 0.8909 (tptt) cc_final: 0.8514 (tttp) REVERT: A 397 LYS cc_start: 0.8420 (pttm) cc_final: 0.8132 (pttp) REVERT: A 401 TYR cc_start: 0.9117 (m-10) cc_final: 0.8881 (m-10) REVERT: A 408 LEU cc_start: 0.8432 (mt) cc_final: 0.8206 (mt) REVERT: A 453 LEU cc_start: 0.8363 (mt) cc_final: 0.8039 (mt) REVERT: A 457 MET cc_start: 0.6781 (mtm) cc_final: 0.6261 (mtm) REVERT: A 459 LEU cc_start: 0.7115 (mt) cc_final: 0.6698 (mt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1801 time to fit residues: 23.9795 Evaluate side-chains 89 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.9524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3398 Z= 0.292 Angle : 0.745 12.641 4603 Z= 0.391 Chirality : 0.046 0.178 520 Planarity : 0.006 0.042 551 Dihedral : 11.082 118.657 453 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.40), residues: 395 helix: 0.55 (0.34), residues: 212 sheet: -1.49 (0.70), residues: 48 loop : -1.25 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 244 HIS 0.006 0.002 HIS A 187 PHE 0.014 0.002 PHE A 55 TYR 0.036 0.003 TYR A 94 ARG 0.005 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8446 (tp) cc_final: 0.7655 (tp) REVERT: A 298 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7474 (tp30) REVERT: A 386 MET cc_start: 0.8625 (tpp) cc_final: 0.8129 (tpp) REVERT: A 397 LYS cc_start: 0.8350 (pttm) cc_final: 0.7710 (pttp) REVERT: A 401 TYR cc_start: 0.9112 (m-10) cc_final: 0.8830 (m-10) REVERT: A 436 ARG cc_start: 0.7837 (mmt180) cc_final: 0.7418 (mmm-85) REVERT: A 437 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 448 LEU cc_start: 0.9504 (pp) cc_final: 0.9224 (pp) REVERT: A 451 MET cc_start: 0.8027 (mtt) cc_final: 0.7408 (mtt) REVERT: A 453 LEU cc_start: 0.8442 (mt) cc_final: 0.8171 (mt) REVERT: A 457 MET cc_start: 0.6760 (mtm) cc_final: 0.6164 (mtm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1453 time to fit residues: 20.4104 Evaluate side-chains 94 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 1.0006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3398 Z= 0.190 Angle : 0.617 9.903 4603 Z= 0.323 Chirality : 0.042 0.138 520 Planarity : 0.004 0.044 551 Dihedral : 10.694 115.942 453 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.42), residues: 395 helix: 1.06 (0.35), residues: 212 sheet: -1.31 (0.66), residues: 58 loop : -1.02 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 82 HIS 0.005 0.001 HIS A 43 PHE 0.035 0.002 PHE A 240 TYR 0.020 0.002 TYR A 94 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8288 (mt) cc_final: 0.7816 (mt) REVERT: A 84 LEU cc_start: 0.8578 (tp) cc_final: 0.8146 (tp) REVERT: A 95 ASN cc_start: 0.8379 (m-40) cc_final: 0.7710 (m110) REVERT: A 97 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7436 (mmmm) REVERT: A 270 MET cc_start: 0.5734 (mmp) cc_final: 0.5523 (mmp) REVERT: A 298 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7307 (tp30) REVERT: A 340 TYR cc_start: 0.8585 (t80) cc_final: 0.8348 (t80) REVERT: A 371 ASP cc_start: 0.8255 (m-30) cc_final: 0.8007 (m-30) REVERT: A 386 MET cc_start: 0.8570 (tpp) cc_final: 0.8125 (tpp) REVERT: A 397 LYS cc_start: 0.8338 (pttm) cc_final: 0.7768 (pttp) REVERT: A 401 TYR cc_start: 0.9057 (m-10) cc_final: 0.8762 (m-10) REVERT: A 437 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 448 LEU cc_start: 0.9499 (pp) cc_final: 0.9278 (pp) REVERT: A 451 MET cc_start: 0.8036 (mtt) cc_final: 0.7370 (mtt) REVERT: A 453 LEU cc_start: 0.8491 (mt) cc_final: 0.8254 (mt) REVERT: A 469 PHE cc_start: 0.7964 (m-10) cc_final: 0.7593 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1646 time to fit residues: 21.5001 Evaluate side-chains 97 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 1.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3398 Z= 0.188 Angle : 0.631 9.881 4603 Z= 0.324 Chirality : 0.042 0.130 520 Planarity : 0.004 0.043 551 Dihedral : 10.474 111.642 453 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.42), residues: 395 helix: 1.28 (0.36), residues: 212 sheet: -0.87 (0.67), residues: 55 loop : -1.05 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 82 HIS 0.006 0.002 HIS A 43 PHE 0.027 0.002 PHE A 240 TYR 0.019 0.002 TYR A 52 ARG 0.003 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7460 (tmt170) cc_final: 0.7161 (ttt-90) REVERT: A 80 ILE cc_start: 0.8325 (mt) cc_final: 0.7831 (mt) REVERT: A 84 LEU cc_start: 0.8491 (tp) cc_final: 0.8191 (tp) REVERT: A 95 ASN cc_start: 0.8329 (m-40) cc_final: 0.7715 (m110) REVERT: A 227 MET cc_start: 0.8415 (tmm) cc_final: 0.8056 (tmm) REVERT: A 231 MET cc_start: 0.6743 (tpp) cc_final: 0.6169 (tpp) REVERT: A 288 GLU cc_start: 0.6050 (tt0) cc_final: 0.5714 (tt0) REVERT: A 298 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7412 (tp30) REVERT: A 371 ASP cc_start: 0.8282 (m-30) cc_final: 0.8035 (m-30) REVERT: A 386 MET cc_start: 0.8597 (tpp) cc_final: 0.8159 (tpp) REVERT: A 397 LYS cc_start: 0.8348 (pttm) cc_final: 0.7748 (pttp) REVERT: A 401 TYR cc_start: 0.9065 (m-10) cc_final: 0.8758 (m-10) REVERT: A 434 ASP cc_start: 0.6235 (t0) cc_final: 0.5986 (t0) REVERT: A 436 ARG cc_start: 0.7741 (mpp-170) cc_final: 0.7354 (mpp80) REVERT: A 437 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6750 (mm-30) REVERT: A 448 LEU cc_start: 0.9505 (pp) cc_final: 0.9259 (pp) REVERT: A 451 MET cc_start: 0.8016 (mtt) cc_final: 0.7331 (mtt) REVERT: A 469 PHE cc_start: 0.8021 (m-10) cc_final: 0.7632 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1612 time to fit residues: 21.9769 Evaluate side-chains 100 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 1.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3398 Z= 0.201 Angle : 0.640 9.957 4603 Z= 0.333 Chirality : 0.042 0.196 520 Planarity : 0.005 0.049 551 Dihedral : 10.370 107.573 453 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.42), residues: 395 helix: 1.42 (0.35), residues: 212 sheet: -0.99 (0.67), residues: 53 loop : -1.10 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 82 HIS 0.008 0.002 HIS A 43 PHE 0.028 0.002 PHE A 404 TYR 0.020 0.002 TYR A 52 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7440 (tmt170) cc_final: 0.7151 (ttt-90) REVERT: A 80 ILE cc_start: 0.8439 (mt) cc_final: 0.7965 (mt) REVERT: A 84 LEU cc_start: 0.8454 (tp) cc_final: 0.8142 (tp) REVERT: A 90 TYR cc_start: 0.6525 (t80) cc_final: 0.6167 (t80) REVERT: A 91 ASN cc_start: 0.7653 (m-40) cc_final: 0.7224 (m-40) REVERT: A 227 MET cc_start: 0.8320 (tmm) cc_final: 0.8058 (tmm) REVERT: A 231 MET cc_start: 0.6777 (tpp) cc_final: 0.6546 (tpp) REVERT: A 288 GLU cc_start: 0.5896 (tt0) cc_final: 0.5633 (tt0) REVERT: A 298 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7459 (tp30) REVERT: A 386 MET cc_start: 0.8717 (tpp) cc_final: 0.8213 (tpp) REVERT: A 397 LYS cc_start: 0.8263 (pttm) cc_final: 0.7705 (pttp) REVERT: A 401 TYR cc_start: 0.9063 (m-10) cc_final: 0.8764 (m-10) REVERT: A 448 LEU cc_start: 0.9512 (pp) cc_final: 0.9307 (pp) REVERT: A 451 MET cc_start: 0.8047 (mtt) cc_final: 0.7357 (mtt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1583 time to fit residues: 21.8649 Evaluate side-chains 105 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.0060 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 1.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3398 Z= 0.178 Angle : 0.634 9.075 4603 Z= 0.330 Chirality : 0.041 0.136 520 Planarity : 0.004 0.042 551 Dihedral : 10.090 102.873 453 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.43), residues: 395 helix: 1.50 (0.35), residues: 212 sheet: -0.86 (0.69), residues: 53 loop : -1.01 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 82 HIS 0.006 0.001 HIS A 43 PHE 0.024 0.002 PHE A 240 TYR 0.023 0.002 TYR A 237 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.394 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 80 ILE cc_start: 0.8542 (mt) cc_final: 0.8098 (mt) REVERT: A 84 LEU cc_start: 0.8319 (tp) cc_final: 0.8097 (tp) REVERT: A 90 TYR cc_start: 0.6319 (t80) cc_final: 0.6021 (t80) REVERT: A 91 ASN cc_start: 0.7667 (m-40) cc_final: 0.7196 (m-40) REVERT: A 227 MET cc_start: 0.8201 (tmm) cc_final: 0.7846 (tmm) REVERT: A 231 MET cc_start: 0.6749 (tpp) cc_final: 0.6499 (tpp) REVERT: A 288 GLU cc_start: 0.5898 (tt0) cc_final: 0.5630 (tt0) REVERT: A 298 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7424 (tp30) REVERT: A 386 MET cc_start: 0.8720 (tpp) cc_final: 0.8241 (tpp) REVERT: A 397 LYS cc_start: 0.8263 (pttm) cc_final: 0.7510 (pttp) REVERT: A 401 TYR cc_start: 0.9006 (m-10) cc_final: 0.8636 (m-10) REVERT: A 436 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: A 451 MET cc_start: 0.8019 (mtt) cc_final: 0.7312 (mtt) REVERT: A 453 LEU cc_start: 0.8722 (mt) cc_final: 0.8518 (mt) REVERT: A 469 PHE cc_start: 0.8042 (m-80) cc_final: 0.7777 (m-80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1601 time to fit residues: 22.4005 Evaluate side-chains 108 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 1.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3398 Z= 0.211 Angle : 0.690 9.808 4603 Z= 0.358 Chirality : 0.043 0.147 520 Planarity : 0.005 0.040 551 Dihedral : 9.909 97.838 453 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.42), residues: 395 helix: 1.15 (0.35), residues: 211 sheet: -1.11 (0.67), residues: 53 loop : -0.99 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 244 HIS 0.006 0.002 HIS A 43 PHE 0.023 0.002 PHE A 240 TYR 0.024 0.002 TYR A 237 ARG 0.003 0.000 ARG A 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8564 (mt) cc_final: 0.8083 (mt) REVERT: A 90 TYR cc_start: 0.6349 (t80) cc_final: 0.6008 (t80) REVERT: A 91 ASN cc_start: 0.7756 (m-40) cc_final: 0.7297 (m-40) REVERT: A 227 MET cc_start: 0.8162 (tmm) cc_final: 0.7858 (tmm) REVERT: A 231 MET cc_start: 0.6910 (tpp) cc_final: 0.6429 (mmt) REVERT: A 288 GLU cc_start: 0.5622 (tt0) cc_final: 0.5182 (tt0) REVERT: A 298 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7458 (tp30) REVERT: A 305 ARG cc_start: 0.6892 (ptt-90) cc_final: 0.5612 (ttm110) REVERT: A 386 MET cc_start: 0.8723 (tpp) cc_final: 0.8199 (tpp) REVERT: A 436 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7485 (mmm-85) REVERT: A 447 LEU cc_start: 0.8357 (tp) cc_final: 0.8157 (tp) REVERT: A 451 MET cc_start: 0.8060 (mtt) cc_final: 0.7394 (mtt) REVERT: A 453 LEU cc_start: 0.8848 (mt) cc_final: 0.8417 (mt) REVERT: A 465 ASN cc_start: 0.8181 (t0) cc_final: 0.7871 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1533 time to fit residues: 21.6226 Evaluate side-chains 103 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.194469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169987 restraints weight = 5968.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176109 restraints weight = 3605.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180808 restraints weight = 2394.811| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 1.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3398 Z= 0.193 Angle : 0.659 9.894 4603 Z= 0.343 Chirality : 0.041 0.141 520 Planarity : 0.004 0.044 551 Dihedral : 9.521 90.892 453 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.42), residues: 395 helix: 1.18 (0.36), residues: 211 sheet: -1.24 (0.67), residues: 53 loop : -0.96 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 244 HIS 0.006 0.001 HIS A 43 PHE 0.040 0.002 PHE A 240 TYR 0.018 0.002 TYR A 52 ARG 0.003 0.000 ARG A 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.18 seconds wall clock time: 20 minutes 56.47 seconds (1256.47 seconds total)