Starting phenix.real_space_refine on Wed Jan 17 13:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/01_2024/8jzr_36751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/01_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_36751/01_2024/8jzr_36751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/01_2024/8jzr_36751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/01_2024/8jzr_36751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzr_36751/01_2024/8jzr_36751.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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 Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.49, per 1000 atoms: 0.72 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 - 3.50 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 436 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 808.8 milliseconds 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: 0.35 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: 1.02 Time building geometry restraints manager: 1.41 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: 97.43 - 104.76: 56 104.76 - 112.09: 1792 112.09 - 119.42: 1128 119.42 - 126.75: 1809 126.75 - 134.09: 52 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 2.440 nonbonded pdb=" O GLN B 485 " pdb=" OG SER B 486 " model vdw 2.381 2.440 nonbonded pdb=" O ALA B 27 " pdb=" N ALA B 29 " model vdw 2.471 2.520 nonbonded pdb=" OD1 ASN B 436 " pdb=" ND1 HIS B 445 " model vdw 2.474 2.520 nonbonded pdb=" O ILE B 542 " pdb=" OG1 THR B 546 " model vdw 2.480 2.440 ... (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: 1.390 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: 0.000 Extract box with map and model: 3.590 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.403 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: 0.2145 time to fit residues: 25.1386 Evaluate side-chains 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7939 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3557 Z= 0.246 Angle : 0.606 6.034 4837 Z= 0.310 Chirality : 0.039 0.139 572 Planarity : 0.005 0.056 592 Dihedral : 4.134 16.881 504 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.81 % Favored : 95.96 % Rotamer: Outliers : 1.42 % Allowed : 12.78 % Favored : 85.80 % 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: 1.50 (0.42), residues: 446 helix: 1.70 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.51 (0.68), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.028 0.002 PHE B 240 TYR 0.015 0.002 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 75 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.383 Fit side-chains REVERT: B 320 LYS cc_start: 0.7797 (mttp) cc_final: 0.7455 (mttt) REVERT: B 326 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 425 LYS cc_start: 0.6333 (ttmt) cc_final: 0.5644 (ttmt) REVERT: B 502 VAL cc_start: 0.8738 (p) cc_final: 0.8474 (t) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.1458 time to fit residues: 13.1633 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 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 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2809 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= 0.206 Angle : 0.552 6.210 4837 Z= 0.282 Chirality : 0.037 0.145 572 Planarity : 0.004 0.055 592 Dihedral : 3.956 14.468 504 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 3.12 % Allowed : 14.49 % Favored : 82.39 % 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: 1.54 (0.41), residues: 446 helix: 1.77 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.05 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.014 0.001 TYR B 113 ARG 0.005 0.001 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 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.368 Fit side-chains REVERT: B 240 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 320 LYS cc_start: 0.7829 (mttp) cc_final: 0.7503 (mttt) REVERT: B 326 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8137 (mp) REVERT: B 425 LYS cc_start: 0.6332 (ttmt) cc_final: 0.5578 (ttmt) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.1407 time to fit residues: 11.4009 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 THR 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 466 ILE 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: 0.7980 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7961 moved from start: 0.3155 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= 0.189 Angle : 0.530 6.104 4837 Z= 0.269 Chirality : 0.036 0.142 572 Planarity : 0.004 0.037 592 Dihedral : 3.856 13.502 504 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.04 % Favored : 95.74 % Rotamer: Outliers : 3.41 % Allowed : 16.48 % Favored : 80.11 % 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: 1.97 (0.42), residues: 446 helix: 2.02 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.47 (0.68), 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 0.016 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.004 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 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.410 Fit side-chains REVERT: B 240 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: B 326 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 425 LYS cc_start: 0.6421 (ttmt) cc_final: 0.5890 (ttmt) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.1290 time to fit residues: 10.9304 Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3557 Z= 0.206 Angle : 0.550 6.190 4837 Z= 0.280 Chirality : 0.037 0.142 572 Planarity : 0.004 0.040 592 Dihedral : 3.903 15.194 504 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.41 % Allowed : 17.33 % Favored : 79.26 % 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: 2.07 (0.41), residues: 446 helix: 2.13 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.59 (0.65), residues: 96 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 0.020 0.002 PHE B 240 TYR 0.015 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 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.384 Fit side-chains REVERT: B 240 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: B 326 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 425 LYS cc_start: 0.6365 (ttmt) cc_final: 0.5874 (ttmt) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.1415 time to fit residues: 11.3485 Evaluate side-chains 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 128 THR 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 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 22 optimal weight: 0.0030 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.0050 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3557 Z= 0.147 Angle : 0.508 5.889 4837 Z= 0.259 Chirality : 0.035 0.139 572 Planarity : 0.004 0.039 592 Dihedral : 3.748 12.623 504 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.84 % Allowed : 18.47 % 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: 2.17 (0.42), residues: 446 helix: 2.24 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.98 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.012 0.001 PHE B 240 TYR 0.009 0.001 TYR B 458 ARG 0.003 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 69 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.389 Fit side-chains REVERT: B 117 MET cc_start: 0.8456 (mmm) cc_final: 0.8184 (mmt) REVERT: B 240 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: B 425 LYS cc_start: 0.6349 (ttmt) cc_final: 0.5636 (ttmt) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1144 time to fit residues: 9.8320 Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 240 PHE Chi-restraints excluded: chain B residue 315 VAL 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=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: 0.3980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3684 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= 0.179 Angle : 0.521 6.208 4837 Z= 0.265 Chirality : 0.036 0.147 572 Planarity : 0.003 0.039 592 Dihedral : 3.744 12.802 504 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.12 % Allowed : 19.03 % 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: 2.26 (0.42), residues: 446 helix: 2.28 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.57 (0.64), residues: 96 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 0.016 0.001 PHE B 240 TYR 0.010 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 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.317 Fit side-chains REVERT: B 240 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: B 326 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 425 LYS cc_start: 0.6360 (ttmt) cc_final: 0.5935 (ttpt) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.1065 time to fit residues: 8.2753 Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 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 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3819 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= 0.209 Angle : 0.544 6.051 4837 Z= 0.278 Chirality : 0.037 0.142 572 Planarity : 0.004 0.040 592 Dihedral : 3.775 13.026 504 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.41 % Allowed : 18.75 % 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: 2.13 (0.41), residues: 446 helix: 2.22 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.68 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** 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 fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.387 Fit side-chains REVERT: B 240 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 320 LYS cc_start: 0.8018 (mttp) cc_final: 0.7776 (mttp) REVERT: B 326 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 425 LYS cc_start: 0.6358 (ttmt) cc_final: 0.5681 (ttmt) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.1447 time to fit residues: 10.9809 Evaluate side-chains 58 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU 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 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.214 > 50: distance: 53 - 70: 13.219 distance: 58 - 74: 23.129 distance: 62 - 80: 5.550 distance: 64 - 65: 5.216 distance: 64 - 67: 5.771 distance: 65 - 70: 6.111 distance: 66 - 91: 3.549 distance: 67 - 69: 4.279 distance: 70 - 71: 6.789 distance: 71 - 72: 9.255 distance: 72 - 73: 14.096 distance: 72 - 74: 15.414 distance: 73 - 98: 7.981 distance: 74 - 75: 23.789 distance: 75 - 76: 3.738 distance: 75 - 78: 18.290 distance: 76 - 80: 8.754 distance: 77 - 102: 12.066 distance: 78 - 79: 16.188 distance: 80 - 81: 5.208 distance: 81 - 84: 5.757 distance: 83 - 108: 4.283 distance: 85 - 86: 6.877 distance: 85 - 87: 5.372 distance: 86 - 88: 4.183 distance: 88 - 90: 6.031 distance: 89 - 90: 5.479 distance: 94 - 112: 4.961 distance: 95 - 97: 4.263 distance: 99 - 100: 3.076 distance: 100 - 101: 3.450 distance: 101 - 120: 6.179 distance: 103 - 104: 3.736 distance: 103 - 106: 3.056 distance: 104 - 108: 3.416 distance: 105 - 128: 5.474 distance: 106 - 107: 3.395 distance: 108 - 109: 4.053 distance: 109 - 110: 3.118 distance: 110 - 111: 3.179 distance: 111 - 133: 3.877 distance: 115 - 140: 4.634 distance: 117 - 119: 4.966 distance: 124 - 125: 4.898 distance: 125 - 126: 4.431 distance: 125 - 127: 8.149