Starting phenix.real_space_refine on Wed Oct 9 18:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_44082.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_44082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_44082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_44082.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1k_44082/10_2024/9b1k_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 3.86, per 1000 atoms: 0.99 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: 1.06 Conformation dependent library (CDL) restraints added in 520.7 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: 0.44 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: 1.22 Time building geometry restraints manager: 1.23 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: 2.840 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.688 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: 0.1723 time to fit residues: 17.9982 Evaluate side-chains 59 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.490 Fit side-chains REVERT: A 22 MET cc_start: 0.7022 (ttm) cc_final: 0.6355 (ttp) REVERT: A 56 ASN cc_start: 0.7343 (t0) cc_final: 0.6919 (t0) REVERT: A 166 ARG cc_start: 0.7637 (ttt180) cc_final: 0.6996 (tpp-160) REVERT: A 231 MET cc_start: 0.7087 (mmm) cc_final: 0.6870 (mmt) REVERT: A 234 ASN cc_start: 0.8754 (t0) cc_final: 0.8546 (t0) REVERT: A 320 VAL cc_start: 0.3640 (OUTLIER) cc_final: 0.3430 (p) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.1466 time to fit residues: 12.8136 Evaluate side-chains 58 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2352 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= 0.203 Angle : 0.551 6.001 5473 Z= 0.277 Chirality : 0.039 0.130 642 Planarity : 0.005 0.040 680 Dihedral : 4.199 15.456 545 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.94 % Allowed : 8.23 % Favored : 89.83 % 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: 0.99 (0.38), residues: 510 helix: 0.87 (0.27), residues: 383 sheet: -2.52 (1.63), residues: 10 loop : 0.67 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 491 HIS 0.002 0.000 HIS A 139 PHE 0.010 0.001 PHE A 358 TYR 0.018 0.001 TYR A 272 ARG 0.004 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 fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.438 Fit side-chains REVERT: A 5 GLU cc_start: 0.6908 (pm20) cc_final: 0.6571 (pm20) REVERT: A 22 MET cc_start: 0.6982 (ttm) cc_final: 0.6754 (mtt) REVERT: A 56 ASN cc_start: 0.7352 (t0) cc_final: 0.6900 (t0) REVERT: A 166 ARG cc_start: 0.7657 (ttt180) cc_final: 0.6998 (tpp-160) REVERT: A 491 TRP cc_start: 0.4795 (t60) cc_final: 0.4541 (p-90) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.1297 time to fit residues: 11.3839 Evaluate side-chains 59 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 34 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2689 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= 0.190 Angle : 0.530 5.733 5473 Z= 0.265 Chirality : 0.038 0.164 642 Planarity : 0.005 0.042 680 Dihedral : 4.036 14.590 545 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 1.17 (0.37), residues: 510 helix: 1.01 (0.26), residues: 381 sheet: -2.44 (1.71), residues: 10 loop : 0.72 (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 0.001 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 76 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.383 Fit side-chains REVERT: A 22 MET cc_start: 0.6980 (ttm) cc_final: 0.6715 (mtt) REVERT: A 56 ASN cc_start: 0.7325 (t0) cc_final: 0.6850 (t0) REVERT: A 166 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7101 (tpp80) REVERT: A 234 ASN cc_start: 0.8642 (t0) cc_final: 0.8276 (t0) REVERT: A 491 TRP cc_start: 0.4925 (t60) cc_final: 0.4721 (p-90) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.1340 time to fit residues: 12.4749 Evaluate side-chains 67 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4011 Z= 0.228 Angle : 0.554 6.798 5473 Z= 0.275 Chirality : 0.039 0.132 642 Planarity : 0.005 0.042 680 Dihedral : 4.057 14.388 545 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.39 % Allowed : 7.99 % Favored : 88.62 % 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: 1.21 (0.38), residues: 510 helix: 0.98 (0.26), residues: 387 sheet: -2.16 (1.86), residues: 10 loop : 0.91 (0.63), 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 0.002 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 74 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.435 Fit side-chains REVERT: A 22 MET cc_start: 0.7009 (ttm) cc_final: 0.6360 (ttp) REVERT: A 56 ASN cc_start: 0.7346 (t0) cc_final: 0.6869 (t0) REVERT: A 166 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7109 (tpp80) REVERT: A 234 ASN cc_start: 0.8660 (t0) cc_final: 0.8450 (t0) REVERT: A 385 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: A 462 MET cc_start: 0.6502 (tpt) cc_final: 0.6103 (tpt) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.1232 time to fit residues: 11.2831 Evaluate side-chains 72 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 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 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 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4011 Z= 0.217 Angle : 0.536 6.833 5473 Z= 0.268 Chirality : 0.038 0.129 642 Planarity : 0.005 0.043 680 Dihedral : 4.044 14.210 545 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.68 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: 1.32 (0.38), residues: 510 helix: 1.05 (0.26), residues: 387 sheet: -2.54 (1.79), residues: 10 loop : 1.02 (0.64), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.001 0.001 HIS A 139 PHE 0.010 0.001 PHE A 358 TYR 0.020 0.001 TYR A 272 ARG 0.002 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 77 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.437 Fit side-chains REVERT: A 22 MET cc_start: 0.7009 (ttm) cc_final: 0.6365 (ttp) REVERT: A 56 ASN cc_start: 0.7361 (t0) cc_final: 0.6877 (t0) REVERT: A 166 ARG cc_start: 0.7694 (ttt180) cc_final: 0.7093 (tpp80) REVERT: A 234 ASN cc_start: 0.8657 (t0) cc_final: 0.8417 (t0) REVERT: A 385 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: A 462 MET cc_start: 0.6547 (tpt) cc_final: 0.6163 (tpt) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.1504 time to fit residues: 14.0364 Evaluate side-chains 73 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 284 ILE 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 Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4011 Z= 0.139 Angle : 0.511 10.444 5473 Z= 0.247 Chirality : 0.036 0.125 642 Planarity : 0.004 0.043 680 Dihedral : 3.783 13.576 545 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.18 % Allowed : 11.14 % Favored : 86.68 % 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: 1.67 (0.38), residues: 510 helix: 1.36 (0.27), residues: 383 sheet: -2.05 (1.94), residues: 10 loop : 0.90 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.016 0.001 TYR A 272 ARG 0.001 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 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 75 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.527 Fit side-chains REVERT: A 22 MET cc_start: 0.6799 (ttm) cc_final: 0.6587 (ptt) REVERT: A 56 ASN cc_start: 0.7306 (t0) cc_final: 0.6797 (t0) REVERT: A 166 ARG cc_start: 0.7687 (ttt180) cc_final: 0.7091 (tpp80) REVERT: A 462 MET cc_start: 0.6377 (tpt) cc_final: 0.6105 (tpt) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1376 time to fit residues: 13.0487 Evaluate side-chains 68 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3399 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= 0.177 Angle : 0.537 7.976 5473 Z= 0.259 Chirality : 0.038 0.146 642 Planarity : 0.004 0.042 680 Dihedral : 3.752 13.209 545 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.66 % Allowed : 10.90 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 510 helix: 1.42 (0.26), residues: 380 sheet: -1.85 (2.07), residues: 10 loop : 0.97 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 275 HIS 0.001 0.000 HIS A 424 PHE 0.010 0.001 PHE A 201 TYR 0.017 0.001 TYR A 272 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 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 70 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.479 Fit side-chains REVERT: A 22 MET cc_start: 0.6883 (ttm) cc_final: 0.6609 (ptt) REVERT: A 56 ASN cc_start: 0.7311 (t0) cc_final: 0.6809 (t0) REVERT: A 166 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7091 (tpp80) REVERT: A 462 MET cc_start: 0.6423 (tpt) cc_final: 0.6116 (tpt) outliers start: 11 outliers final: 11 residues processed: 66 average time/residue: 0.1697 time to fit residues: 14.7214 Evaluate side-chains 67 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 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 210 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 451 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4011 Z= 0.190 Angle : 0.545 7.239 5473 Z= 0.264 Chirality : 0.038 0.145 642 Planarity : 0.004 0.042 680 Dihedral : 3.755 13.163 545 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.15 % Allowed : 10.41 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.38), residues: 510 helix: 1.45 (0.27), residues: 378 sheet: -1.94 (2.03), residues: 10 loop : 1.16 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 424 PHE 0.009 0.001 PHE A 266 TYR 0.017 0.001 TYR A 272 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 9 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 71 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.442 Fit side-chains REVERT: A 22 MET cc_start: 0.6915 (ttm) cc_final: 0.6583 (ptt) REVERT: A 56 ASN cc_start: 0.7332 (t0) cc_final: 0.6845 (t0) REVERT: A 166 ARG cc_start: 0.7730 (ttt180) cc_final: 0.7095 (tpp80) REVERT: A 462 MET cc_start: 0.6458 (tpt) cc_final: 0.6094 (tpt) outliers start: 13 outliers final: 13 residues processed: 66 average time/residue: 0.1287 time to fit residues: 11.4094 Evaluate side-chains 70 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3547 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 : 0.549 6.729 5473 Z= 0.264 Chirality : 0.038 0.131 642 Planarity : 0.004 0.042 680 Dihedral : 3.675 12.766 545 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.39 % Allowed : 10.65 % Favored : 85.96 % 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: 1.90 (0.38), residues: 510 helix: 1.51 (0.27), residues: 380 sheet: -2.03 (1.96), residues: 10 loop : 1.06 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 139 PHE 0.010 0.001 PHE A 201 TYR 0.017 0.001 TYR A 272 ARG 0.001 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 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 72 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.625 Fit side-chains REVERT: A 22 MET cc_start: 0.6928 (ttm) cc_final: 0.6646 (ptt) REVERT: A 56 ASN cc_start: 0.7319 (t0) cc_final: 0.6830 (t0) REVERT: A 166 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7082 (tpp80) REVERT: A 462 MET cc_start: 0.6415 (tpt) cc_final: 0.6051 (tpt) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 0.1363 time to fit residues: 12.3111 Evaluate side-chains 69 residues out of total 413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 210 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 374 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.193179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152068 restraints weight = 4616.697| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.17 r_work: 0.3425 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4011 Z= 0.198 Angle : 0.552 6.762 5473 Z= 0.266 Chirality : 0.039 0.128 642 Planarity : 0.004 0.042 680 Dihedral : 3.718 12.770 545 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.15 % Allowed : 10.41 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.38), residues: 510 helix: 1.52 (0.27), residues: 378 sheet: -2.08 (1.97), residues: 10 loop : 1.14 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.001 0.000 HIS A 424 PHE 0.009 0.001 PHE A 266 TYR 0.018 0.001 TYR A 272 ARG 0.002 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.21 seconds wall clock time: 33 minutes 58.67 seconds (2038.67 seconds total)