Starting phenix.real_space_refine on Thu Jun 5 06:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.map" model { file = "/net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gv5_51624/06_2025/9gv5_51624.cif" } resolution = 4.0 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 1806 2.51 5 N 421 2.21 5 O 446 1.98 5 H 2766 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5465 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 5465 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 15, 'TRANS': 339} Chain breaks: 2 Time building chain proxies: 3.46, per 1000 atoms: 0.63 Number of scatterers: 5465 At special positions: 0 Unit cell: (67.32, 65.824, 65.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 446 8.00 N 421 7.00 C 1806 6.00 H 2766 1.00 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: 1.43 Conformation dependent library (CDL) restraints added in 436.9 milliseconds 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 632 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 89.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.658A pdb=" N PHE A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 157 removed outlier: 4.180A pdb=" N ALA A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 187 removed outlier: 3.895A pdb=" N ILE A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ARG A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.879A pdb=" N LEU A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.745A pdb=" N VAL A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.967A pdb=" N TYR A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 254 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 266 through 277 removed outlier: 4.298A pdb=" N MET A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.867A pdb=" N GLY A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.939A pdb=" N GLU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 4.914A pdb=" N THR A 366 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 removed outlier: 4.056A pdb=" N LYS A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 386 through 403 removed outlier: 3.837A pdb=" N GLN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.630A pdb=" N ARG A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.941A pdb=" N VAL A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 443 through 471 removed outlier: 4.309A pdb=" N LEU A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Proline residue: A 458 - end of helix Proline residue: A 463 - end of helix removed outlier: 4.502A pdb=" N ASN A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 484 through 491 197 hydrogen bonds defined for protein. 591 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: 1.74 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2756 1.03 - 1.23: 10 1.23 - 1.42: 1173 1.42 - 1.61: 1558 1.61 - 1.81: 42 Bond restraints: 5539 Sorted by residual: bond pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta sigma weight residual 1.454 1.443 0.012 1.23e-02 6.61e+03 8.76e-01 bond pdb=" CA VAL A 485 " pdb=" CB VAL A 485 " ideal model delta sigma weight residual 1.534 1.539 -0.005 6.80e-03 2.16e+04 4.96e-01 bond pdb=" CA GLY A 112 " pdb=" C GLY A 112 " ideal model delta sigma weight residual 1.517 1.510 0.008 1.08e-02 8.57e+03 4.86e-01 bond pdb=" CA LYS A 258 " pdb=" C LYS A 258 " ideal model delta sigma weight residual 1.523 1.532 -0.008 1.34e-02 5.57e+03 3.96e-01 bond pdb=" CG GLN A 390 " pdb=" CD GLN A 390 " ideal model delta sigma weight residual 1.516 1.503 0.013 2.50e-02 1.60e+03 2.71e-01 ... (remaining 5534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 9194 1.01 - 2.03: 764 2.03 - 3.04: 42 3.04 - 4.06: 11 4.06 - 5.07: 3 Bond angle restraints: 10014 Sorted by residual: angle pdb=" N ILE A 363 " pdb=" CA ILE A 363 " pdb=" C ILE A 363 " ideal model delta sigma weight residual 112.96 108.75 4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" C ALA A 491 " pdb=" N VAL A 492 " pdb=" CA VAL A 492 " ideal model delta sigma weight residual 122.97 120.90 2.07 9.80e-01 1.04e+00 4.48e+00 angle pdb=" N CYS A 472 " pdb=" CA CYS A 472 " pdb=" C CYS A 472 " ideal model delta sigma weight residual 112.72 110.30 2.42 1.28e+00 6.10e-01 3.58e+00 angle pdb=" N SER A 188 " pdb=" CA SER A 188 " pdb=" C SER A 188 " ideal model delta sigma weight residual 113.23 111.00 2.23 1.22e+00 6.72e-01 3.35e+00 angle pdb=" CA ILE A 363 " pdb=" C ILE A 363 " pdb=" N GLY A 364 " ideal model delta sigma weight residual 118.65 116.83 1.82 1.07e+00 8.73e-01 2.90e+00 ... (remaining 10009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2384 17.13 - 34.25: 145 34.25 - 51.38: 48 51.38 - 68.51: 46 68.51 - 85.63: 1 Dihedral angle restraints: 2624 sinusoidal: 1367 harmonic: 1257 Sorted by residual: dihedral pdb=" CA TYR A 335 " pdb=" C TYR A 335 " pdb=" N PHE A 336 " pdb=" CA PHE A 336 " ideal model delta harmonic sigma weight residual 180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA THR A 187 " pdb=" C THR A 187 " pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA PHE A 155 " pdb=" C PHE A 155 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " ideal model delta harmonic sigma weight residual -180.00 -164.59 -15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 2621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 280 0.026 - 0.052: 83 0.052 - 0.078: 42 0.078 - 0.104: 24 0.104 - 0.130: 4 Chirality restraints: 433 Sorted by residual: chirality pdb=" CA ILE A 353 " pdb=" N ILE A 353 " pdb=" C ILE A 353 " pdb=" CB ILE A 353 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE A 381 " pdb=" N ILE A 381 " pdb=" C ILE A 381 " pdb=" CB ILE A 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PRO A 338 " pdb=" N PRO A 338 " pdb=" C PRO A 338 " pdb=" CB PRO A 338 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 430 not shown) Planarity restraints: 796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 463 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 464 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 485 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 486 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 199 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C PHE A 199 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 199 " 0.008 2.00e-02 2.50e+03 pdb=" N THR A 200 " 0.007 2.00e-02 2.50e+03 ... (remaining 793 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 842 2.28 - 2.86: 12553 2.86 - 3.44: 14256 3.44 - 4.02: 17868 4.02 - 4.60: 27977 Nonbonded interactions: 73496 Sorted by model distance: nonbonded pdb=" O GLU A 355 " pdb=" H LEU A 359 " model vdw 1.696 2.450 nonbonded pdb="HH11 ARG A 171 " pdb=" O LEU A 278 " model vdw 1.700 2.450 nonbonded pdb=" O MET A 274 " pdb=" HG SER A 277 " model vdw 1.708 2.450 nonbonded pdb=" O LYS A 386 " pdb=" H LEU A 389 " model vdw 1.748 2.450 nonbonded pdb=" O LYS A 385 " pdb=" H TYR A 388 " model vdw 1.821 2.450 ... (remaining 73491 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: 1.720 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.440 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 : 0.002 0.022 2773 Z= 0.122 Angle : 0.522 5.075 3760 Z= 0.306 Chirality : 0.037 0.130 433 Planarity : 0.004 0.039 459 Dihedral : 11.201 85.633 945 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.35 % Allowed : 4.21 % Favored : 95.44 % 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: 0.71 (0.48), residues: 349 helix: 1.29 (0.33), residues: 262 sheet: None (None), residues: 0 loop : -2.07 (0.71), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 109 HIS 0.002 0.001 HIS A 186 PHE 0.012 0.001 PHE A 182 TYR 0.012 0.001 TYR A 125 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.09153 ( 197) hydrogen bonds : angle 5.55211 ( 591) covalent geometry : bond 0.00224 ( 2773) covalent geometry : angle 0.52167 ( 3760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LYS cc_start: 0.7575 (tppt) cc_final: 0.7366 (mmmt) REVERT: A 274 MET cc_start: 0.8157 (ttp) cc_final: 0.7361 (tpp) REVERT: A 403 MET cc_start: 0.5926 (tpp) cc_final: 0.5616 (tpp) REVERT: A 408 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6150 (tpt170) REVERT: A 437 GLU cc_start: 0.7526 (tp30) cc_final: 0.7325 (tp30) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.2357 time to fit residues: 24.6150 Evaluate side-chains 71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.158312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.134979 restraints weight = 21305.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.141337 restraints weight = 10472.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.145503 restraints weight = 6131.565| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2773 Z= 0.145 Angle : 0.544 4.956 3760 Z= 0.302 Chirality : 0.038 0.132 433 Planarity : 0.005 0.037 459 Dihedral : 4.744 18.717 373 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.35 % Allowed : 11.58 % Favored : 88.07 % 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: 0.45 (0.46), residues: 349 helix: 1.17 (0.32), residues: 259 sheet: None (None), residues: 0 loop : -2.28 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 109 HIS 0.003 0.001 HIS A 186 PHE 0.012 0.001 PHE A 426 TYR 0.011 0.001 TYR A 125 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 197) hydrogen bonds : angle 5.42670 ( 591) covalent geometry : bond 0.00285 ( 2773) covalent geometry : angle 0.54377 ( 3760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.428 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: symmetry clash REVERT: A 274 MET cc_start: 0.8828 (ttp) cc_final: 0.7894 (tpp) REVERT: A 339 TYR cc_start: 0.7262 (t80) cc_final: 0.7050 (t80) REVERT: A 403 MET cc_start: 0.5673 (tpp) cc_final: 0.5408 (tpp) REVERT: A 408 ARG cc_start: 0.6788 (mtp85) cc_final: 0.5955 (tpt170) REVERT: A 455 MET cc_start: 0.9465 (mtp) cc_final: 0.9120 (mpp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2328 time to fit residues: 21.2632 Evaluate side-chains 66 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.156977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133544 restraints weight = 21442.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.140019 restraints weight = 10513.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144209 restraints weight = 6075.863| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2773 Z= 0.148 Angle : 0.550 4.864 3760 Z= 0.305 Chirality : 0.038 0.137 433 Planarity : 0.004 0.037 459 Dihedral : 4.698 16.995 373 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.70 % Allowed : 11.93 % Favored : 87.37 % 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: 0.34 (0.46), residues: 349 helix: 1.00 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -2.15 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 109 HIS 0.003 0.001 HIS A 186 PHE 0.010 0.001 PHE A 182 TYR 0.010 0.001 TYR A 125 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 197) hydrogen bonds : angle 5.43410 ( 591) covalent geometry : bond 0.00282 ( 2773) covalent geometry : angle 0.55020 ( 3760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.419 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8053 (mmp) cc_final: 0.7808 (mmp) REVERT: A 274 MET cc_start: 0.8877 (ttp) cc_final: 0.7956 (tpp) REVERT: A 403 MET cc_start: 0.5715 (tpp) cc_final: 0.5436 (tpp) REVERT: A 408 ARG cc_start: 0.6822 (mtp85) cc_final: 0.6054 (tpt170) REVERT: A 455 MET cc_start: 0.9501 (mtp) cc_final: 0.9128 (mpp) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.2613 time to fit residues: 22.8839 Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.4298 r_free = 0.4298 target = 0.157123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133917 restraints weight = 21581.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.140494 restraints weight = 10468.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.144723 restraints weight = 6000.389| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2773 Z= 0.149 Angle : 0.549 4.824 3760 Z= 0.303 Chirality : 0.037 0.136 433 Planarity : 0.004 0.037 459 Dihedral : 4.674 17.463 373 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.70 % Allowed : 14.39 % Favored : 84.91 % 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: 0.34 (0.46), residues: 349 helix: 0.98 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -2.09 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 109 HIS 0.003 0.001 HIS A 186 PHE 0.011 0.001 PHE A 224 TYR 0.009 0.001 TYR A 125 ARG 0.001 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 197) hydrogen bonds : angle 5.42210 ( 591) covalent geometry : bond 0.00285 ( 2773) covalent geometry : angle 0.54855 ( 3760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.415 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8058 (mmp) cc_final: 0.7786 (mmp) REVERT: A 274 MET cc_start: 0.8892 (ttp) cc_final: 0.7879 (tpp) REVERT: A 403 MET cc_start: 0.5730 (tpp) cc_final: 0.5451 (tpp) REVERT: A 408 ARG cc_start: 0.6863 (mtp85) cc_final: 0.6064 (tpt170) REVERT: A 451 LEU cc_start: 0.9261 (tp) cc_final: 0.9039 (tp) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.2537 time to fit residues: 21.8877 Evaluate side-chains 70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.158363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.135110 restraints weight = 21330.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.141626 restraints weight = 10444.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.145864 restraints weight = 6033.718| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2773 Z= 0.123 Angle : 0.531 4.942 3760 Z= 0.288 Chirality : 0.037 0.139 433 Planarity : 0.004 0.038 459 Dihedral : 4.543 16.783 373 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.35 % Allowed : 14.39 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.47), residues: 349 helix: 1.17 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -1.92 (0.73), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 109 HIS 0.004 0.001 HIS A 186 PHE 0.011 0.001 PHE A 182 TYR 0.009 0.001 TYR A 201 ARG 0.001 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 197) hydrogen bonds : angle 5.26508 ( 591) covalent geometry : bond 0.00243 ( 2773) covalent geometry : angle 0.53057 ( 3760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8071 (mmp) cc_final: 0.7753 (mmp) REVERT: A 274 MET cc_start: 0.8885 (ttp) cc_final: 0.7870 (tpp) REVERT: A 403 MET cc_start: 0.5697 (tpp) cc_final: 0.5431 (tpp) REVERT: A 408 ARG cc_start: 0.6851 (mtp85) cc_final: 0.6050 (tpt170) REVERT: A 451 LEU cc_start: 0.9291 (tp) cc_final: 0.9084 (tp) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.2515 time to fit residues: 22.3989 Evaluate side-chains 72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.134584 restraints weight = 21556.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141020 restraints weight = 10680.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.145373 restraints weight = 6210.210| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2773 Z= 0.128 Angle : 0.534 4.824 3760 Z= 0.292 Chirality : 0.037 0.136 433 Planarity : 0.005 0.043 459 Dihedral : 4.496 16.471 373 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.70 % Allowed : 15.44 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.47), residues: 349 helix: 1.12 (0.32), residues: 265 sheet: None (None), residues: 0 loop : -1.75 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 109 HIS 0.004 0.001 HIS A 186 PHE 0.010 0.001 PHE A 182 TYR 0.008 0.001 TYR A 201 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 197) hydrogen bonds : angle 5.25040 ( 591) covalent geometry : bond 0.00255 ( 2773) covalent geometry : angle 0.53385 ( 3760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.419 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: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8054 (mmp) cc_final: 0.7726 (mmp) REVERT: A 274 MET cc_start: 0.8879 (ttp) cc_final: 0.7970 (tpp) REVERT: A 403 MET cc_start: 0.5750 (tpp) cc_final: 0.5524 (tpp) REVERT: A 408 ARG cc_start: 0.6880 (mtp85) cc_final: 0.6052 (tpt170) REVERT: A 451 LEU cc_start: 0.9278 (tp) cc_final: 0.9067 (tp) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2494 time to fit residues: 22.1733 Evaluate side-chains 71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.157926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.135149 restraints weight = 21119.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.141490 restraints weight = 10216.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.145716 restraints weight = 5898.408| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2773 Z= 0.133 Angle : 0.537 4.780 3760 Z= 0.294 Chirality : 0.037 0.137 433 Planarity : 0.005 0.041 459 Dihedral : 4.451 15.866 373 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.70 % Allowed : 16.14 % Favored : 83.16 % 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: 0.65 (0.47), residues: 349 helix: 1.11 (0.32), residues: 266 sheet: None (None), residues: 0 loop : -1.72 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 109 HIS 0.004 0.001 HIS A 186 PHE 0.010 0.001 PHE A 182 TYR 0.009 0.001 TYR A 201 ARG 0.001 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 197) hydrogen bonds : angle 5.23578 ( 591) covalent geometry : bond 0.00263 ( 2773) covalent geometry : angle 0.53659 ( 3760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.414 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8096 (mmp) cc_final: 0.7756 (mmp) REVERT: A 274 MET cc_start: 0.8847 (ttp) cc_final: 0.7939 (tpp) REVERT: A 403 MET cc_start: 0.5753 (tpp) cc_final: 0.5516 (tpp) REVERT: A 408 ARG cc_start: 0.6901 (mtp85) cc_final: 0.6063 (tpt170) REVERT: A 451 LEU cc_start: 0.9307 (tp) cc_final: 0.9096 (tp) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.2477 time to fit residues: 21.8826 Evaluate side-chains 70 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.4296 r_free = 0.4296 target = 0.156708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.133772 restraints weight = 21402.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140136 restraints weight = 10399.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.144362 restraints weight = 5990.365| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2773 Z= 0.149 Angle : 0.554 5.753 3760 Z= 0.306 Chirality : 0.038 0.136 433 Planarity : 0.005 0.038 459 Dihedral : 4.496 15.819 373 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.70 % Allowed : 16.84 % Favored : 82.46 % 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: 0.48 (0.47), residues: 349 helix: 0.99 (0.32), residues: 266 sheet: None (None), residues: 0 loop : -1.80 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.003 0.001 HIS A 186 PHE 0.011 0.001 PHE A 224 TYR 0.010 0.001 TYR A 201 ARG 0.001 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 197) hydrogen bonds : angle 5.30052 ( 591) covalent geometry : bond 0.00290 ( 2773) covalent geometry : angle 0.55419 ( 3760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.425 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8126 (mmp) cc_final: 0.7801 (mmp) REVERT: A 274 MET cc_start: 0.8823 (ttp) cc_final: 0.7899 (tpp) REVERT: A 403 MET cc_start: 0.5751 (tpp) cc_final: 0.5518 (tpp) REVERT: A 408 ARG cc_start: 0.6850 (mtp85) cc_final: 0.6042 (tpt170) REVERT: A 451 LEU cc_start: 0.9312 (tp) cc_final: 0.9105 (tp) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.2564 time to fit residues: 22.0961 Evaluate side-chains 71 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.4295 r_free = 0.4295 target = 0.156659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133556 restraints weight = 21505.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.139849 restraints weight = 10356.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144036 restraints weight = 5974.603| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2773 Z= 0.154 Angle : 0.562 4.800 3760 Z= 0.313 Chirality : 0.037 0.136 433 Planarity : 0.004 0.038 459 Dihedral : 4.528 15.973 373 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.70 % Allowed : 17.19 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.47), residues: 349 helix: 0.98 (0.32), residues: 266 sheet: None (None), residues: 0 loop : -1.82 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.003 0.001 HIS A 186 PHE 0.012 0.001 PHE A 224 TYR 0.009 0.001 TYR A 201 ARG 0.002 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 197) hydrogen bonds : angle 5.35987 ( 591) covalent geometry : bond 0.00296 ( 2773) covalent geometry : angle 0.56175 ( 3760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.402 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: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8105 (mmp) cc_final: 0.7783 (mmp) REVERT: A 274 MET cc_start: 0.8789 (ttp) cc_final: 0.7846 (tpp) REVERT: A 403 MET cc_start: 0.5679 (tpp) cc_final: 0.5436 (tpp) REVERT: A 408 ARG cc_start: 0.6826 (mtp85) cc_final: 0.6026 (tpt170) REVERT: A 451 LEU cc_start: 0.9307 (tp) cc_final: 0.9093 (tp) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.2493 time to fit residues: 21.8969 Evaluate side-chains 68 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.4307 r_free = 0.4307 target = 0.157427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.134491 restraints weight = 21563.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.140949 restraints weight = 10397.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.145145 restraints weight = 5958.395| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2773 Z= 0.135 Angle : 0.566 6.134 3760 Z= 0.309 Chirality : 0.037 0.135 433 Planarity : 0.005 0.039 459 Dihedral : 4.497 16.798 373 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.70 % Allowed : 17.89 % Favored : 81.40 % 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: 0.61 (0.47), residues: 349 helix: 1.07 (0.32), residues: 266 sheet: None (None), residues: 0 loop : -1.72 (0.77), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 109 HIS 0.004 0.001 HIS A 186 PHE 0.009 0.001 PHE A 224 TYR 0.011 0.001 TYR A 201 ARG 0.001 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 197) hydrogen bonds : angle 5.36175 ( 591) covalent geometry : bond 0.00280 ( 2773) covalent geometry : angle 0.56579 ( 3760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.804 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8086 (mmp) cc_final: 0.7754 (mmp) REVERT: A 274 MET cc_start: 0.8774 (ttp) cc_final: 0.7805 (tpp) REVERT: A 403 MET cc_start: 0.5679 (tpp) cc_final: 0.5436 (tpp) REVERT: A 408 ARG cc_start: 0.6807 (mtp85) cc_final: 0.6017 (tpt170) REVERT: A 451 LEU cc_start: 0.9305 (tp) cc_final: 0.9102 (tp) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2838 time to fit residues: 25.7464 Evaluate side-chains 72 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 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 = 0.4305 r_free = 0.4305 target = 0.157372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.133868 restraints weight = 21564.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.140222 restraints weight = 10523.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.144567 restraints weight = 6135.255| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2773 Z= 0.157 Angle : 0.570 4.791 3760 Z= 0.316 Chirality : 0.037 0.135 433 Planarity : 0.005 0.037 459 Dihedral : 4.527 16.170 373 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.70 % Allowed : 18.25 % Favored : 81.05 % 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: 0.44 (0.47), residues: 349 helix: 0.97 (0.33), residues: 266 sheet: None (None), residues: 0 loop : -1.84 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.003 0.001 HIS A 222 PHE 0.012 0.001 PHE A 224 TYR 0.012 0.001 TYR A 201 ARG 0.001 0.000 ARG A 322 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 197) hydrogen bonds : angle 5.43560 ( 591) covalent geometry : bond 0.00311 ( 2773) covalent geometry : angle 0.57048 ( 3760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.34 seconds wall clock time: 46 minutes 41.36 seconds (2801.36 seconds total)