Starting phenix.real_space_refine on Wed Mar 5 22:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.map" model { file = "/net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ly6_4118/03_2025/5ly6_4118.cif" } resolution = 4.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 139 atoms to isotropic. 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 7 5.16 5 C 2350 2.51 5 N 633 2.21 5 O 735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3725 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3725 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 452} Time building chain proxies: 3.50, per 1000 atoms: 0.94 Number of scatterers: 3725 At special positions: 0 Unit cell: (85.4, 78.4, 127.4, 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 7 16.00 O 735 8.00 N 633 7.00 C 2350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.90 Conformation dependent library (CDL) restraints added in 450.4 milliseconds 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 12.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.880A pdb=" N ARG B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.669A pdb=" N ARG B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=A, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.614A pdb=" N ARG B 31 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 44 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 43 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 357 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 45 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 355 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 353 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=C, first strand: chain 'B' and resid 147 through 149 removed outlier: 3.577A pdb=" N GLU B 258 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 191 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 250 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 197 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 152 through 165 Processing sheet with id=E, first strand: chain 'B' and resid 235 through 237 removed outlier: 4.147A pdb=" N TYR B 331 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 345 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 261 through 264 Processing sheet with id=G, first strand: chain 'B' and resid 408 through 413 removed outlier: 4.183A pdb=" N ARG B 451 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 364 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 368 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 457 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.910A pdb=" N VAL B 372 " --> pdb=" O CYS B 428 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'B' and resid 382 through 384 Processing sheet with id=J, first strand: chain 'B' and resid 440 through 442 removed outlier: 4.087A pdb=" N TYR B 440 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 425 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS B 442 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 423 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 419 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 380 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 421 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=J 101 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1239 1.34 - 1.46: 424 1.46 - 1.57: 2121 1.57 - 1.69: 1 1.69 - 1.81: 13 Bond restraints: 3798 Sorted by residual: bond pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 1.332 1.597 -0.265 1.29e-02 6.01e+03 4.22e+02 bond pdb=" N PRO B 413 " pdb=" CD PRO B 413 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" C ILE B 412 " pdb=" N PRO B 413 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.86e+00 bond pdb=" CA ALA B 64 " pdb=" CB ALA B 64 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.55e-02 4.16e+03 3.44e+00 bond pdb=" C HIS B 324 " pdb=" O HIS B 324 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.58e+00 ... (remaining 3793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 5147 5.44 - 10.88: 9 10.88 - 16.33: 4 16.33 - 21.77: 0 21.77 - 27.21: 4 Bond angle restraints: 5164 Sorted by residual: angle pdb=" O THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 123.24 111.38 11.86 1.23e+00 6.61e-01 9.30e+01 angle pdb=" CA THR B 57 " pdb=" C THR B 57 " pdb=" N SER B 58 " ideal model delta sigma weight residual 115.58 126.98 -11.40 1.48e+00 4.57e-01 5.93e+01 angle pdb=" C LEU B 39 " pdb=" N PRO B 40 " pdb=" CD PRO B 40 " ideal model delta sigma weight residual 125.00 97.79 27.21 4.10e+00 5.95e-02 4.40e+01 angle pdb=" C ASP B 117 " pdb=" N PRO B 118 " pdb=" CD PRO B 118 " ideal model delta sigma weight residual 125.00 99.67 25.33 4.10e+00 5.95e-02 3.82e+01 angle pdb=" C ALA B 273 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 125.00 102.20 22.80 4.10e+00 5.95e-02 3.09e+01 ... (remaining 5159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 1777 17.28 - 34.56: 264 34.56 - 51.85: 163 51.85 - 69.13: 64 69.13 - 86.41: 18 Dihedral angle restraints: 2286 sinusoidal: 905 harmonic: 1381 Sorted by residual: dihedral pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " pdb=" CG ASN B 30 " pdb=" OD1 ASN B 30 " ideal model delta sinusoidal sigma weight residual -90.00 -161.80 71.80 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -159.76 69.76 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 135.95 44.05 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 498 0.033 - 0.067: 17 0.067 - 0.100: 65 0.100 - 0.133: 4 0.133 - 0.167: 6 Chirality restraints: 590 Sorted by residual: chirality pdb=" CB THR B 63 " pdb=" CA THR B 63 " pdb=" OG1 THR B 63 " pdb=" CG2 THR B 63 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CB THR B 65 " pdb=" CA THR B 65 " pdb=" OG1 THR B 65 " pdb=" CG2 THR B 65 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ALA B 12 " pdb=" N ALA B 12 " pdb=" C ALA B 12 " pdb=" CB ALA B 12 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 587 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 39 " -0.120 5.00e-02 4.00e+02 1.91e-01 5.81e+01 pdb=" N PRO B 40 " 0.329 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 117 " -0.116 5.00e-02 4.00e+02 1.84e-01 5.42e+01 pdb=" N PRO B 118 " 0.318 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 273 " 0.111 5.00e-02 4.00e+02 1.76e-01 4.93e+01 pdb=" N PRO B 274 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " 0.084 5.00e-02 4.00e+02 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 20 2.20 - 2.88: 1637 2.88 - 3.55: 4768 3.55 - 4.23: 7738 4.23 - 4.90: 12540 Nonbonded interactions: 26703 Sorted by model distance: nonbonded pdb=" CG1 VAL B 78 " pdb=" CD PRO B 233 " model vdw 1.526 3.860 nonbonded pdb=" OD1 ASP B 295 " pdb=" ND1 HIS B 324 " model vdw 1.808 3.120 nonbonded pdb=" CG2 VAL B 302 " pdb=" CD1 LEU B 313 " model vdw 1.854 3.880 nonbonded pdb=" N LEU B 76 " pdb=" O VAL B 235 " model vdw 1.876 3.120 nonbonded pdb=" CG1 VAL B 78 " pdb=" CG PRO B 233 " model vdw 1.894 3.860 ... (remaining 26698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 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 0.265 3798 Z= 0.393 Angle : 1.237 27.209 5164 Z= 0.692 Chirality : 0.034 0.167 590 Planarity : 0.018 0.191 668 Dihedral : 24.278 86.412 1394 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 94.62 Ramachandran Plot: Outliers : 4.90 % Allowed : 20.90 % Favored : 74.20 % Rotamer: Outliers : 36.32 % Allowed : 24.94 % Favored : 38.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -5.32 (0.32), residues: 469 helix: -1.20 (0.61), residues: 63 sheet: -2.85 (0.35), residues: 189 loop : -4.99 (0.27), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 436 HIS 0.000 0.000 HIS B 135 PHE 0.001 0.000 PHE B 9 TYR 0.003 0.000 TYR B 15 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 64 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8383 (t) REVERT: B 106 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8530 (pt) REVERT: B 151 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5919 (tp30) REVERT: B 194 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7211 (t0) REVERT: B 236 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8151 (p90) REVERT: B 288 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.5882 (mmtt) REVERT: B 349 ASP cc_start: 0.7404 (p0) cc_final: 0.7117 (p0) REVERT: B 448 VAL cc_start: 0.4786 (OUTLIER) cc_final: 0.4353 (p) outliers start: 150 outliers final: 33 residues processed: 192 average time/residue: 0.2151 time to fit residues: 48.2790 Evaluate side-chains 87 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 47 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 245 GLN B 324 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.051572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.044107 restraints weight = 35811.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045126 restraints weight = 23188.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.045863 restraints weight = 16501.402| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 3798 Z= 0.344 Angle : 0.858 8.938 5164 Z= 0.448 Chirality : 0.049 0.240 590 Planarity : 0.009 0.105 668 Dihedral : 5.479 26.234 509 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.51 % Favored : 87.63 % Rotamer: Outliers : 0.48 % Allowed : 5.57 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -4.14 (0.35), residues: 469 helix: -0.58 (0.68), residues: 61 sheet: -2.00 (0.37), residues: 183 loop : -4.13 (0.32), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 134 HIS 0.007 0.002 HIS B 156 PHE 0.020 0.002 PHE B 335 TYR 0.026 0.003 TYR B 199 ARG 0.005 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7071 (t-90) cc_final: 0.6483 (t70) REVERT: B 336 LEU cc_start: 0.9082 (tp) cc_final: 0.8730 (pt) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.1909 time to fit residues: 9.7410 Evaluate side-chains 24 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 156 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.047559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040298 restraints weight = 38329.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041256 restraints weight = 24134.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041931 restraints weight = 17068.824| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 3798 Z= 0.453 Angle : 0.881 7.189 5164 Z= 0.468 Chirality : 0.048 0.213 590 Planarity : 0.008 0.086 668 Dihedral : 6.151 32.549 509 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.64 % Allowed : 13.22 % Favored : 86.14 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.14 (0.34), residues: 469 helix: -1.42 (0.56), residues: 73 sheet: -1.89 (0.35), residues: 199 loop : -4.20 (0.32), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 134 HIS 0.013 0.003 HIS B 135 PHE 0.015 0.003 PHE B 43 TYR 0.031 0.004 TYR B 15 ARG 0.004 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7224 (t-90) cc_final: 0.6725 (t-90) REVERT: B 336 LEU cc_start: 0.9360 (tp) cc_final: 0.9147 (tp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2373 time to fit residues: 8.3234 Evaluate side-chains 19 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.040603 restraints weight = 38272.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041533 restraints weight = 24321.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.042207 restraints weight = 17347.055| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 3798 Z= 0.315 Angle : 0.757 14.975 5164 Z= 0.384 Chirality : 0.044 0.242 590 Planarity : 0.007 0.103 668 Dihedral : 5.641 27.513 509 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.02 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.51 (0.36), residues: 469 helix: -1.27 (0.60), residues: 66 sheet: -1.73 (0.33), residues: 225 loop : -3.42 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 278 HIS 0.009 0.002 HIS B 135 PHE 0.011 0.002 PHE B 335 TYR 0.019 0.002 TYR B 15 ARG 0.008 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7459 (t-90) cc_final: 0.6975 (t-90) REVERT: B 336 LEU cc_start: 0.9334 (tp) cc_final: 0.9078 (tp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1974 time to fit residues: 6.2116 Evaluate side-chains 20 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.0050 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.048431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041294 restraints weight = 39231.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.042256 restraints weight = 24209.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.042943 restraints weight = 16959.713| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3798 Z= 0.240 Angle : 0.671 10.340 5164 Z= 0.344 Chirality : 0.044 0.180 590 Planarity : 0.007 0.120 668 Dihedral : 5.479 31.030 509 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.02 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 5.88 % 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: -3.11 (0.37), residues: 469 helix: -0.82 (0.61), residues: 71 sheet: -1.36 (0.33), residues: 227 loop : -3.51 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 134 HIS 0.007 0.002 HIS B 135 PHE 0.013 0.002 PHE B 335 TYR 0.021 0.002 TYR B 331 ARG 0.009 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7260 (t-90) cc_final: 0.6836 (t-90) REVERT: B 97 MET cc_start: 0.8982 (mmm) cc_final: 0.8667 (tpp) REVERT: B 336 LEU cc_start: 0.9354 (tp) cc_final: 0.8752 (pp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1932 time to fit residues: 6.0807 Evaluate side-chains 17 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.047390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.040254 restraints weight = 37969.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041204 restraints weight = 23669.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041864 restraints weight = 16674.558| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 1.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3798 Z= 0.284 Angle : 0.671 8.618 5164 Z= 0.344 Chirality : 0.043 0.142 590 Planarity : 0.007 0.121 668 Dihedral : 5.519 23.552 509 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.09 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.37), residues: 469 helix: -0.81 (0.62), residues: 65 sheet: -1.24 (0.34), residues: 211 loop : -3.11 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 134 HIS 0.012 0.002 HIS B 135 PHE 0.013 0.002 PHE B 43 TYR 0.014 0.002 TYR B 15 ARG 0.007 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7330 (t-90) cc_final: 0.6937 (t-90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1886 time to fit residues: 5.6911 Evaluate side-chains 17 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.045949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038856 restraints weight = 39049.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039762 restraints weight = 24997.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.040386 restraints weight = 17885.502| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 1.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 3798 Z= 0.375 Angle : 0.759 7.428 5164 Z= 0.394 Chirality : 0.044 0.143 590 Planarity : 0.008 0.138 668 Dihedral : 6.021 22.628 509 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.37 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.25 (0.36), residues: 469 helix: -1.34 (0.64), residues: 59 sheet: -1.44 (0.33), residues: 214 loop : -3.19 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 278 HIS 0.015 0.002 HIS B 135 PHE 0.018 0.003 PHE B 43 TYR 0.023 0.003 TYR B 371 ARG 0.014 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 HIS cc_start: 0.7494 (t-90) cc_final: 0.7163 (t-90) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2302 time to fit residues: 6.5285 Evaluate side-chains 18 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.047152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040191 restraints weight = 40148.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041157 restraints weight = 24918.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.041804 restraints weight = 17460.770| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 1.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3798 Z= 0.235 Angle : 0.644 7.497 5164 Z= 0.330 Chirality : 0.043 0.141 590 Planarity : 0.008 0.154 668 Dihedral : 5.529 20.652 509 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.09 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.16 (0.36), residues: 469 helix: -1.15 (0.64), residues: 59 sheet: -1.45 (0.33), residues: 218 loop : -3.12 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 278 HIS 0.008 0.002 HIS B 135 PHE 0.012 0.001 PHE B 43 TYR 0.014 0.002 TYR B 15 ARG 0.012 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.9362 (tp) cc_final: 0.8778 (pp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2156 time to fit residues: 6.7806 Evaluate side-chains 19 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.047451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.040217 restraints weight = 38266.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041187 restraints weight = 24351.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041872 restraints weight = 17394.593| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 1.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3798 Z= 0.182 Angle : 0.613 7.366 5164 Z= 0.311 Chirality : 0.043 0.166 590 Planarity : 0.006 0.115 668 Dihedral : 5.140 19.381 509 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.81 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.37), residues: 469 helix: -0.87 (0.64), residues: 59 sheet: -1.13 (0.34), residues: 223 loop : -3.02 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 278 HIS 0.005 0.001 HIS B 135 PHE 0.012 0.001 PHE B 43 TYR 0.015 0.001 TYR B 15 ARG 0.010 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1690 time to fit residues: 5.9966 Evaluate side-chains 18 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.040836 restraints weight = 38549.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041799 restraints weight = 24541.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.042490 restraints weight = 17535.090| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 1.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 3798 Z= 0.162 Angle : 0.598 7.044 5164 Z= 0.301 Chirality : 0.044 0.155 590 Planarity : 0.006 0.106 668 Dihedral : 4.934 18.774 509 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.53 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.38), residues: 469 helix: -0.77 (0.62), residues: 65 sheet: -0.94 (0.35), residues: 223 loop : -2.90 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.003 0.001 HIS B 135 PHE 0.009 0.001 PHE B 43 TYR 0.014 0.001 TYR B 15 ARG 0.010 0.001 ARG B 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.438 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1755 time to fit residues: 6.0287 Evaluate side-chains 17 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.045916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.038908 restraints weight = 39738.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.039812 restraints weight = 25422.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.040416 restraints weight = 18226.143| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 1.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3798 Z= 0.277 Angle : 0.666 6.308 5164 Z= 0.343 Chirality : 0.044 0.209 590 Planarity : 0.008 0.150 668 Dihedral : 5.356 20.466 509 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.09 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.38), residues: 469 helix: -0.89 (0.68), residues: 53 sheet: -1.09 (0.34), residues: 223 loop : -2.60 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 278 HIS 0.007 0.002 HIS B 135 PHE 0.014 0.002 PHE B 43 TYR 0.022 0.002 TYR B 15 ARG 0.012 0.001 ARG B 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1472.32 seconds wall clock time: 26 minutes 36.89 seconds (1596.89 seconds total)