Starting phenix.real_space_refine on Thu Nov 14 03:09:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/11_2024/8jzr_36751.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.060 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2304 2.51 5 N 562 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3474 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3460 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.90 Number of scatterers: 3474 At special positions: 0 Unit cell: (82.0652, 56.9432, 67.8294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 590 8.00 N 562 7.00 C 2304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 436 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 834 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 81.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 34 through 57 removed outlier: 3.501A pdb=" N GLY B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 4.034A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 212 removed outlier: 3.989A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.629A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.503A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.849A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 4.132A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 372 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.866A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.953A pdb=" N LYS B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.589A pdb=" N TYR B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 759 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: 0.94 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 525 1.30 - 1.43: 963 1.43 - 1.55: 2041 1.55 - 1.68: 1 1.68 - 1.81: 27 Bond restraints: 3557 Sorted by residual: bond pdb=" CA ALA B 35 " pdb=" C ALA B 35 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.32e-02 5.74e+03 4.17e+01 bond pdb=" CA ALA B 36 " pdb=" C ALA B 36 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.09e+01 bond pdb=" C ALA B 36 " pdb=" O ALA B 36 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.00e+01 bond pdb=" CA ALA B 31 " pdb=" C ALA B 31 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.34e-02 5.57e+03 2.41e+01 bond pdb=" C CYS B 37 " pdb=" O CYS B 37 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.16e-02 7.43e+03 1.89e+01 ... (remaining 3552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4684 1.92 - 3.84: 117 3.84 - 5.75: 28 5.75 - 7.67: 6 7.67 - 9.59: 2 Bond angle restraints: 4837 Sorted by residual: angle pdb=" C GLY B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta sigma weight residual 121.86 131.24 -9.38 1.65e+00 3.67e-01 3.23e+01 angle pdb=" N ARG B 34 " pdb=" CA ARG B 34 " pdb=" C ARG B 34 " ideal model delta sigma weight residual 113.97 107.79 6.18 1.28e+00 6.10e-01 2.33e+01 angle pdb=" C ALA B 31 " pdb=" N GLY B 32 " pdb=" CA GLY B 32 " ideal model delta sigma weight residual 119.98 114.70 5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" N PHE B 30 " pdb=" CA PHE B 30 " pdb=" C PHE B 30 " ideal model delta sigma weight residual 110.80 101.21 9.59 2.13e+00 2.20e-01 2.03e+01 angle pdb=" CA CYS B 37 " pdb=" C CYS B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 117.02 122.14 -5.12 1.17e+00 7.31e-01 1.91e+01 ... (remaining 4832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1827 14.97 - 29.95: 184 29.95 - 44.92: 48 44.92 - 59.90: 6 59.90 - 74.87: 2 Dihedral angle restraints: 2067 sinusoidal: 766 harmonic: 1301 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.10 35.90 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA PRO B 390 " pdb=" C PRO B 390 " pdb=" N ILE B 391 " pdb=" CA ILE B 391 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" N ARG B 33 " pdb=" C ARG B 33 " pdb=" CA ARG B 33 " pdb=" CB ARG B 33 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 506 0.065 - 0.130: 54 0.130 - 0.196: 7 0.196 - 0.261: 4 0.261 - 0.326: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" CA CYS B 37 " pdb=" N CYS B 37 " pdb=" C CYS B 37 " pdb=" CB CYS B 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ALA B 31 " pdb=" N ALA B 31 " pdb=" C ALA B 31 " pdb=" CB ALA B 31 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PHE B 30 " pdb=" N PHE B 30 " pdb=" C PHE B 30 " pdb=" CB PHE B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 569 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 389 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.82e+00 pdb=" N PRO B 390 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 28 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C GLY B 28 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY B 28 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 29 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 187 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 188 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.032 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1313 2.88 - 3.39: 3603 3.39 - 3.89: 5787 3.89 - 4.40: 6562 4.40 - 4.90: 11119 Nonbonded interactions: 28384 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" OG1 THR B 85 " model vdw 2.381 3.040 nonbonded pdb=" O GLN B 485 " pdb=" OG SER B 486 " model vdw 2.381 3.040 nonbonded pdb=" O ALA B 27 " pdb=" N ALA B 29 " model vdw 2.471 3.120 nonbonded pdb=" OD1 ASN B 436 " pdb=" ND1 HIS B 445 " model vdw 2.474 3.120 nonbonded pdb=" O ILE B 542 " pdb=" OG1 THR B 546 " model vdw 2.480 3.040 ... (remaining 28379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.190 Find NCS groups from input model: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.007 0.085 3557 Z= 0.441 Angle : 0.772 9.589 4837 Z= 0.460 Chirality : 0.048 0.326 572 Planarity : 0.006 0.078 592 Dihedral : 12.737 74.870 1230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.81 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.75 (0.42), residues: 446 helix: 1.17 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.001 0.000 HIS B 348 PHE 0.020 0.001 PHE B 237 TYR 0.015 0.001 TYR B 335 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.370 Fit side-chains REVERT: B 502 VAL cc_start: 0.8649 (p) cc_final: 0.8417 (t) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2156 time to fit residues: 25.2721 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3557 Z= 0.213 Angle : 0.590 5.966 4837 Z= 0.303 Chirality : 0.039 0.142 572 Planarity : 0.005 0.058 592 Dihedral : 4.125 16.909 504 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 12.78 % Favored : 86.08 % 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: 1.51 (0.42), residues: 446 helix: 1.72 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.51 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.025 0.002 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.004 0.001 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.387 Fit side-chains REVERT: B 82 MET cc_start: 0.8202 (mmt) cc_final: 0.7949 (mmt) REVERT: B 320 LYS cc_start: 0.7735 (mttp) cc_final: 0.7430 (mttt) REVERT: B 326 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 425 LYS cc_start: 0.6322 (ttmt) cc_final: 0.5656 (ttmt) REVERT: B 502 VAL cc_start: 0.8711 (p) cc_final: 0.8310 (t) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.1378 time to fit residues: 13.0503 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3557 Z= 0.180 Angle : 0.545 6.120 4837 Z= 0.279 Chirality : 0.037 0.145 572 Planarity : 0.004 0.055 592 Dihedral : 3.935 15.458 504 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.14 % Favored : 96.64 % Rotamer: Outliers : 3.41 % Allowed : 15.06 % Favored : 81.53 % 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: 1.60 (0.41), residues: 446 helix: 1.84 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.20 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.001 HIS B 348 PHE 0.017 0.001 PHE B 240 TYR 0.011 0.001 TYR B 113 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.359 Fit side-chains REVERT: B 184 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8377 (ttpt) REVERT: B 320 LYS cc_start: 0.7805 (mttp) cc_final: 0.7487 (mttt) REVERT: B 326 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 425 LYS cc_start: 0.6366 (ttmt) cc_final: 0.5704 (ttmt) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.1500 time to fit residues: 13.5459 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 27 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3557 Z= 0.175 Angle : 0.531 6.104 4837 Z= 0.271 Chirality : 0.036 0.143 572 Planarity : 0.004 0.040 592 Dihedral : 3.853 14.312 504 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 17.90 % Favored : 78.98 % 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: 1.78 (0.41), residues: 446 helix: 1.98 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.16 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.012 0.001 PHE B 240 TYR 0.011 0.001 TYR B 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.345 Fit side-chains REVERT: B 184 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8366 (ttpt) REVERT: B 326 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 425 LYS cc_start: 0.6329 (ttmt) cc_final: 0.5561 (ttmt) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1537 time to fit residues: 14.0429 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3557 Z= 0.202 Angle : 0.566 8.097 4837 Z= 0.282 Chirality : 0.038 0.234 572 Planarity : 0.004 0.038 592 Dihedral : 3.842 14.044 504 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 18.75 % Favored : 78.12 % 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: 1.92 (0.41), residues: 446 helix: 2.07 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -2.15 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.010 0.001 PHE B 492 TYR 0.012 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.328 Fit side-chains REVERT: B 326 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 425 LYS cc_start: 0.6348 (ttmt) cc_final: 0.5781 (ttmt) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1276 time to fit residues: 9.9699 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3557 Z= 0.202 Angle : 0.553 6.329 4837 Z= 0.278 Chirality : 0.037 0.142 572 Planarity : 0.004 0.038 592 Dihedral : 3.863 13.761 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.69 % Allowed : 18.18 % Favored : 78.12 % 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: 2.12 (0.41), residues: 446 helix: 2.19 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.74 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.009 0.001 PHE B 194 TYR 0.013 0.001 TYR B 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: B 326 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 425 LYS cc_start: 0.6377 (ttmt) cc_final: 0.5655 (ttmt) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.1291 time to fit residues: 11.1793 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3557 Z= 0.172 Angle : 0.532 6.046 4837 Z= 0.269 Chirality : 0.037 0.143 572 Planarity : 0.004 0.038 592 Dihedral : 3.788 13.486 504 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.56 % Allowed : 18.75 % Favored : 78.69 % 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: 2.05 (0.41), residues: 446 helix: 2.20 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.22 (0.59), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 453 HIS 0.001 0.000 HIS B 348 PHE 0.011 0.001 PHE B 372 TYR 0.009 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.8510 (mmm) cc_final: 0.8263 (mmt) REVERT: B 240 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 326 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 425 LYS cc_start: 0.6363 (ttmt) cc_final: 0.5533 (ttmt) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1239 time to fit residues: 10.2172 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3557 Z= 0.197 Angle : 0.541 6.115 4837 Z= 0.275 Chirality : 0.037 0.139 572 Planarity : 0.004 0.039 592 Dihedral : 3.806 13.425 504 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.12 % Allowed : 19.32 % Favored : 77.56 % 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: 2.20 (0.42), residues: 446 helix: 2.25 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.80 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS B 348 PHE 0.010 0.001 PHE B 492 TYR 0.011 0.001 TYR B 113 ARG 0.003 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.8562 (mmm) cc_final: 0.8359 (mmt) REVERT: B 240 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: B 326 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8200 (mp) REVERT: B 425 LYS cc_start: 0.6313 (ttmt) cc_final: 0.5724 (ttpt) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1178 time to fit residues: 9.3220 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3557 Z= 0.172 Angle : 0.536 6.014 4837 Z= 0.270 Chirality : 0.037 0.144 572 Planarity : 0.003 0.037 592 Dihedral : 3.769 13.018 504 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.56 % Allowed : 19.03 % Favored : 78.41 % 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: 2.24 (0.42), residues: 446 helix: 2.30 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.82 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 453 HIS 0.001 0.000 HIS B 348 PHE 0.012 0.001 PHE B 372 TYR 0.009 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: B 326 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 425 LYS cc_start: 0.6304 (ttmt) cc_final: 0.5710 (ttpt) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.1431 time to fit residues: 11.5164 Evaluate side-chains 59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3557 Z= 0.211 Angle : 0.573 9.728 4837 Z= 0.286 Chirality : 0.038 0.154 572 Planarity : 0.004 0.037 592 Dihedral : 3.832 13.094 504 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.27 % Allowed : 19.03 % Favored : 78.69 % 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: 2.23 (0.42), residues: 446 helix: 2.29 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.83 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.011 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.003 0.000 ARG B 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 425 LYS cc_start: 0.6371 (ttmt) cc_final: 0.5582 (ttpt) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.1492 time to fit residues: 10.7486 Evaluate side-chains 58 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.0040 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130251 restraints weight = 4269.268| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.04 r_work: 0.3347 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3557 Z= 0.209 Angle : 0.580 11.451 4837 Z= 0.287 Chirality : 0.038 0.179 572 Planarity : 0.004 0.037 592 Dihedral : 3.867 13.244 504 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.56 % Allowed : 19.60 % Favored : 77.84 % 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: 2.14 (0.42), residues: 446 helix: 2.22 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.80 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.012 0.001 PHE B 372 TYR 0.012 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1141.86 seconds wall clock time: 21 minutes 12.70 seconds (1272.70 seconds total)