Starting phenix.real_space_refine on Mon Jan 13 20:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1k_44082/01_2025/9b1k_44082.cif" } resolution = 3.3 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= 0.001 sd= 0.016 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 30 5.16 5 C 2548 2.51 5 N 661 2.21 5 O 672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3911 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3899 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 29, 'TRANS': 482} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.67, per 1000 atoms: 0.94 Number of scatterers: 3911 At special positions: 0 Unit cell: (57.761, 102.542, 89.562, 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 30 16.00 O 672 8.00 N 661 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " 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 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 514.0 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 944 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.512A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.515A pdb=" N ALA A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.786A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.965A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.622A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.717A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 222 No H-bonds generated for 'chain 'A' and resid 221 through 222' Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.297A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.828A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 4.080A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 removed outlier: 4.163A pdb=" N GLN A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.911A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.536A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.518A pdb=" N VAL A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 3.561A pdb=" N PHE A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.572A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.613A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 455 Processing helix chain 'A' and resid 460 through 485 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.933A pdb=" N VAL A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.758A pdb=" N LEU A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 269 hydrogen bonds defined for protein. 777 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: 1.13 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1232 1.34 - 1.46: 955 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4011 Sorted by residual: bond pdb=" C2 URC A 901 " pdb=" O11 URC A 901 " ideal model delta sigma weight residual 1.213 1.360 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 1.215 1.350 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C4 URC A 901 " pdb=" C5 URC A 901 " ideal model delta sigma weight residual 1.358 1.488 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 URC A 901 " pdb=" O13 URC A 901 " ideal model delta sigma weight residual 1.218 1.345 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C4 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 4006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 5417 2.68 - 5.35: 44 5.35 - 8.03: 5 8.03 - 10.70: 4 10.70 - 13.38: 3 Bond angle restraints: 5473 Sorted by residual: angle pdb=" N1 URC A 901 " pdb=" C2 URC A 901 " pdb=" N3 URC A 901 " ideal model delta sigma weight residual 114.62 128.00 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C2 URC A 901 " pdb=" N1 URC A 901 " pdb=" C6 URC A 901 " ideal model delta sigma weight residual 129.31 117.61 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" N9 URC A 901 " ideal model delta sigma weight residual 104.73 116.27 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5 URC A 901 " pdb=" C6 URC A 901 " pdb=" N1 URC A 901 " ideal model delta sigma weight residual 111.19 121.73 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N7 URC A 901 " pdb=" C8 URC A 901 " pdb=" O24 URC A 901 " ideal model delta sigma weight residual 129.09 119.74 9.35 3.00e+00 1.11e-01 9.72e+00 ... (remaining 5468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 2189 15.54 - 31.08: 143 31.08 - 46.62: 16 46.62 - 62.16: 5 62.16 - 77.70: 2 Dihedral angle restraints: 2355 sinusoidal: 892 harmonic: 1463 Sorted by residual: dihedral pdb=" CA GLU A 329 " pdb=" C GLU A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 286 " pdb=" C LYS A 286 " pdb=" N GLY A 287 " pdb=" CA GLY A 287 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " pdb=" CE MET A 36 " ideal model delta sinusoidal sigma weight residual 180.00 129.26 50.74 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 2352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 380 0.026 - 0.053: 177 0.053 - 0.079: 52 0.079 - 0.105: 25 0.105 - 0.131: 8 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL A 422 " pdb=" N VAL A 422 " pdb=" C VAL A 422 " pdb=" CB VAL A 422 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL A 118 " pdb=" N VAL A 118 " pdb=" C VAL A 118 " pdb=" CB VAL A 118 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 639 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 276 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 277 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 265 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 480 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.015 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 968 2.79 - 3.32: 3936 3.32 - 3.85: 6497 3.85 - 4.37: 7738 4.37 - 4.90: 12839 Nonbonded interactions: 31978 Sorted by model distance: nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.265 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.346 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.410 3.040 nonbonded pdb=" O PHE A 270 " pdb=" OG SER A 273 " model vdw 2.411 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.424 3.040 ... (remaining 31973 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: 3.070 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.006 0.147 4011 Z= 0.375 Angle : 0.739 13.375 5473 Z= 0.354 Chirality : 0.037 0.131 642 Planarity : 0.004 0.034 680 Dihedral : 10.547 77.700 1405 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: 0.11 (0.37), residues: 510 helix: 0.05 (0.26), residues: 375 sheet: -1.86 (1.54), residues: 10 loop : 0.91 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 491 HIS 0.002 0.000 HIS A 83 PHE 0.014 0.001 PHE A 270 TYR 0.011 0.001 TYR A 272 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.7160 (ttm) cc_final: 0.6490 (ttp) REVERT: A 56 ASN cc_start: 0.7463 (t0) cc_final: 0.7147 (t0) REVERT: A 166 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7178 (tpp80) REVERT: A 231 MET cc_start: 0.7036 (mmm) cc_final: 0.6787 (mmt) REVERT: A 234 ASN cc_start: 0.8722 (t0) cc_final: 0.8462 (t0) REVERT: A 291 GLN cc_start: 0.7796 (mt0) cc_final: 0.7228 (tt0) REVERT: A 367 LEU cc_start: 0.8448 (mt) cc_final: 0.8182 (mp) REVERT: A 374 ILE cc_start: 0.7877 (pt) cc_final: 0.7643 (tt) REVERT: A 491 TRP cc_start: 0.4952 (t60) cc_final: 0.4749 (t60) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1538 time to fit residues: 15.8618 Evaluate side-chains 59 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.190910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148146 restraints weight = 4578.042| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.28 r_work: 0.3401 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4011 Z= 0.206 Angle : 0.571 5.662 5473 Z= 0.293 Chirality : 0.039 0.133 642 Planarity : 0.005 0.047 680 Dihedral : 4.411 16.247 545 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 6.54 % Favored : 91.77 % 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: 0.96 (0.38), residues: 510 helix: 0.72 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.79 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 50 HIS 0.002 0.001 HIS A 424 PHE 0.010 0.001 PHE A 358 TYR 0.017 0.002 TYR A 272 ARG 0.011 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.433 Fit side-chains REVERT: A 22 MET cc_start: 0.6875 (ttm) cc_final: 0.6192 (ttp) REVERT: A 56 ASN cc_start: 0.7208 (t0) cc_final: 0.6784 (t0) REVERT: A 166 ARG cc_start: 0.7636 (ttt180) cc_final: 0.6920 (tpp-160) REVERT: A 231 MET cc_start: 0.6994 (mmm) cc_final: 0.6748 (mmt) REVERT: A 320 VAL cc_start: 0.3604 (OUTLIER) cc_final: 0.3399 (p) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.1404 time to fit residues: 12.1216 Evaluate side-chains 57 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 399 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.189606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145553 restraints weight = 4614.905| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.36 r_work: 0.3395 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4011 Z= 0.195 Angle : 0.548 6.188 5473 Z= 0.275 Chirality : 0.038 0.130 642 Planarity : 0.005 0.040 680 Dihedral : 4.183 15.449 545 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.94 % Allowed : 8.47 % Favored : 89.59 % 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: 1.06 (0.38), residues: 510 helix: 0.92 (0.27), residues: 380 sheet: -2.48 (1.63), residues: 10 loop : 0.69 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 491 HIS 0.002 0.000 HIS A 139 PHE 0.009 0.001 PHE A 358 TYR 0.018 0.001 TYR A 272 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.350 Fit side-chains REVERT: A 5 GLU cc_start: 0.6796 (pm20) cc_final: 0.6446 (pm20) REVERT: A 22 MET cc_start: 0.6824 (ttm) cc_final: 0.6590 (mtt) REVERT: A 56 ASN cc_start: 0.7213 (t0) cc_final: 0.6758 (t0) REVERT: A 166 ARG cc_start: 0.7647 (ttt180) cc_final: 0.6923 (tpp-160) REVERT: A 491 TRP cc_start: 0.4817 (t60) cc_final: 0.4489 (p-90) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1216 time to fit residues: 10.6076 Evaluate side-chains 60 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 42 optimal weight: 0.0060 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.186804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142960 restraints weight = 4613.578| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.31 r_work: 0.3389 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4011 Z= 0.187 Angle : 0.523 5.724 5473 Z= 0.263 Chirality : 0.038 0.174 642 Planarity : 0.005 0.042 680 Dihedral : 4.033 14.557 545 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.15 % Allowed : 7.26 % Favored : 89.59 % 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: 1.20 (0.37), residues: 510 helix: 1.03 (0.26), residues: 381 sheet: -2.44 (1.71), residues: 10 loop : 0.71 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 491 HIS 0.002 0.001 HIS A 139 PHE 0.009 0.001 PHE A 358 TYR 0.019 0.001 TYR A 272 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.447 Fit side-chains REVERT: A 22 MET cc_start: 0.6818 (ttm) cc_final: 0.6537 (mtt) REVERT: A 56 ASN cc_start: 0.7195 (t0) cc_final: 0.6713 (t0) REVERT: A 166 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7000 (tpp80) REVERT: A 234 ASN cc_start: 0.8620 (t0) cc_final: 0.8303 (t0) REVERT: A 491 TRP cc_start: 0.4974 (t60) cc_final: 0.4678 (p-90) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.1339 time to fit residues: 12.8806 Evaluate side-chains 68 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.191904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148688 restraints weight = 4696.008| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.35 r_work: 0.3369 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4011 Z= 0.219 Angle : 0.550 6.818 5473 Z= 0.274 Chirality : 0.039 0.135 642 Planarity : 0.005 0.042 680 Dihedral : 4.026 14.413 545 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.63 % Allowed : 8.47 % Favored : 87.89 % 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: 1.27 (0.38), residues: 510 helix: 1.01 (0.26), residues: 387 sheet: -2.30 (1.82), residues: 10 loop : 0.98 (0.64), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.002 0.001 HIS A 139 PHE 0.011 0.001 PHE A 358 TYR 0.020 0.001 TYR A 272 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.423 Fit side-chains REVERT: A 22 MET cc_start: 0.6847 (ttm) cc_final: 0.6191 (ttp) REVERT: A 56 ASN cc_start: 0.7230 (t0) cc_final: 0.6755 (t0) REVERT: A 166 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7002 (tpp80) REVERT: A 385 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: A 462 MET cc_start: 0.6323 (tpt) cc_final: 0.5962 (tpt) REVERT: A 491 TRP cc_start: 0.4931 (t60) cc_final: 0.4679 (p-90) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.1274 time to fit residues: 11.9687 Evaluate side-chains 71 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.184100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139514 restraints weight = 4677.861| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.36 r_work: 0.3388 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4011 Z= 0.177 Angle : 0.512 6.789 5473 Z= 0.255 Chirality : 0.038 0.132 642 Planarity : 0.004 0.042 680 Dihedral : 3.910 13.933 545 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.39 % Allowed : 9.20 % Favored : 87.41 % 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: 1.45 (0.38), residues: 510 helix: 1.19 (0.26), residues: 388 sheet: -2.51 (1.81), residues: 10 loop : 0.90 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.009 0.001 PHE A 201 TYR 0.018 0.001 TYR A 272 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.437 Fit side-chains REVERT: A 22 MET cc_start: 0.6751 (ttm) cc_final: 0.6366 (ptt) REVERT: A 56 ASN cc_start: 0.7215 (t0) cc_final: 0.6718 (t0) REVERT: A 166 ARG cc_start: 0.7649 (ttt180) cc_final: 0.6974 (tpp80) REVERT: A 234 ASN cc_start: 0.8533 (t0) cc_final: 0.8326 (t0) REVERT: A 385 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: A 462 MET cc_start: 0.6297 (tpt) cc_final: 0.5988 (tpt) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.1220 time to fit residues: 11.0127 Evaluate side-chains 74 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-dev-5571/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-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1213 > 50: distance: 2 - 23: 14.159 distance: 7 - 31: 19.524 distance: 12 - 36: 28.578 distance: 18 - 23: 12.572 distance: 19 - 44: 21.819 distance: 23 - 24: 6.271 distance: 24 - 25: 17.877 distance: 24 - 27: 17.287 distance: 25 - 31: 10.454 distance: 26 - 52: 7.949 distance: 27 - 28: 4.268 distance: 31 - 32: 6.931 distance: 32 - 33: 5.371 distance: 32 - 35: 9.401 distance: 33 - 34: 7.844 distance: 33 - 36: 3.943 distance: 34 - 59: 3.588 distance: 36 - 37: 3.096 distance: 37 - 40: 10.829 distance: 38 - 39: 7.267 distance: 38 - 44: 12.308 distance: 39 - 65: 43.520 distance: 40 - 41: 13.058 distance: 41 - 42: 7.263 distance: 41 - 43: 12.771 distance: 44 - 45: 10.296 distance: 45 - 46: 5.622 distance: 45 - 48: 10.821 distance: 46 - 47: 12.314 distance: 46 - 52: 4.797 distance: 47 - 73: 37.431 distance: 48 - 49: 4.953 distance: 49 - 50: 10.842 distance: 50 - 51: 7.681 distance: 52 - 53: 4.216 distance: 53 - 54: 13.456 distance: 53 - 56: 17.352 distance: 54 - 55: 10.966 distance: 54 - 59: 3.991 distance: 55 - 81: 22.364 distance: 56 - 57: 11.156 distance: 56 - 58: 18.808 distance: 60 - 61: 19.140 distance: 60 - 63: 12.383 distance: 61 - 62: 29.253 distance: 61 - 65: 34.752 distance: 62 - 95: 23.021 distance: 63 - 64: 33.138 distance: 65 - 66: 52.042 distance: 66 - 67: 15.921 distance: 66 - 69: 25.671 distance: 67 - 68: 21.318 distance: 67 - 73: 12.639 distance: 68 - 103: 21.231 distance: 69 - 70: 15.951 distance: 70 - 72: 20.212 distance: 73 - 74: 20.143 distance: 74 - 75: 9.614 distance: 74 - 77: 12.357 distance: 75 - 76: 8.729 distance: 75 - 81: 8.406 distance: 76 - 109: 21.603 distance: 77 - 78: 6.600 distance: 78 - 79: 10.635 distance: 79 - 80: 26.751 distance: 82 - 83: 11.144 distance: 82 - 85: 5.275 distance: 83 - 84: 11.658 distance: 83 - 95: 13.131 distance: 84 - 116: 21.998 distance: 85 - 86: 7.011 distance: 86 - 87: 7.402 distance: 86 - 88: 7.110 distance: 87 - 89: 5.593 distance: 88 - 90: 14.203 distance: 88 - 91: 6.471 distance: 89 - 90: 7.817 distance: 90 - 92: 7.318 distance: 91 - 93: 8.842 distance: 92 - 94: 7.287 distance: 93 - 94: 8.151 distance: 95 - 96: 7.296 distance: 96 - 97: 4.189 distance: 96 - 99: 14.762 distance: 97 - 103: 4.658 distance: 98 - 123: 7.463 distance: 99 - 100: 11.109 distance: 100 - 101: 30.401 distance: 100 - 102: 21.169 distance: 151 - 160: 3.443