Starting phenix.real_space_refine on Mon Sep 23 18:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ski_10225/09_2024/6ski_10225.cif" } resolution = 2.6 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2818 2.51 5 N 776 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4434 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4092 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 498} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 342 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.69, per 1000 atoms: 0.83 Number of scatterers: 4434 At special positions: 0 Unit cell: (65.536, 71.68, 124.928, 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 19 16.00 O 821 8.00 N 776 7.00 C 2818 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: 1.04 Conformation dependent library (CDL) restraints added in 527.3 milliseconds 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 8 sheets defined 32.5% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'F' and resid 52 through 59 Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.149A pdb=" N THR F 148 " --> pdb=" O MET F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.580A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 348 Processing helix chain 'F' and resid 349 through 363 Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 388 through 395 Processing helix chain 'F' and resid 415 through 432 removed outlier: 3.771A pdb=" N VAL F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 451 through 467 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.726A pdb=" N ILE F 533 " --> pdb=" O ASP F 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 4 through 9 removed outlier: 4.316A pdb=" N TYR F 4 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE F 184 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG F 33 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE F 186 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 35 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 188 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N VAL F 238 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N ILE F 189 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N PHE F 240 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE F 191 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY F 242 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL F 193 " --> pdb=" O GLY F 242 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N LYS F 278 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG F 239 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE F 280 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU F 241 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 282 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU F 243 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA F 284 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU F 304 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN F 281 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU F 306 " --> pdb=" O GLN F 281 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR F 283 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 121 through 128 Processing sheet with id=AA3, first strand: chain 'F' and resid 294 through 296 removed outlier: 6.612A pdb=" N LEU F 294 " --> pdb=" O TRP F 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 328 through 331 Processing sheet with id=AA5, first strand: chain 'F' and resid 328 through 331 removed outlier: 4.568A pdb=" N GLN F 398 " --> pdb=" O VAL F 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AA7, first strand: chain 'F' and resid 500 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 806 through 809 184 hydrogen bonds defined for protein. 516 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: 1.27 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1472 1.34 - 1.46: 874 1.46 - 1.57: 2150 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4528 Sorted by residual: bond pdb=" C LYS F 29 " pdb=" N LYS F 30 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 4.01e+00 bond pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 1.521 1.499 0.021 1.27e-02 6.20e+03 2.86e+00 bond pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta sigma weight residual 1.447 1.423 0.024 1.58e-02 4.01e+03 2.35e+00 bond pdb=" CA ASP F 245 " pdb=" C ASP F 245 " ideal model delta sigma weight residual 1.533 1.519 0.014 9.60e-03 1.09e+04 2.08e+00 bond pdb=" C SER F 197 " pdb=" N ARG F 198 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.42e-02 4.96e+03 1.72e+00 ... (remaining 4523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 6001 2.13 - 4.26: 106 4.26 - 6.40: 7 6.40 - 8.53: 3 8.53 - 10.66: 2 Bond angle restraints: 6119 Sorted by residual: angle pdb=" C PHE F 196 " pdb=" N SER F 197 " pdb=" CA SER F 197 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N ARG F 198 " pdb=" CA ARG F 198 " pdb=" C ARG F 198 " ideal model delta sigma weight residual 113.97 109.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" N SER F 197 " pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 110.80 117.52 -6.72 2.13e+00 2.20e-01 9.95e+00 angle pdb=" C GLY F 199 " pdb=" N ALA F 200 " pdb=" CA ALA F 200 " ideal model delta sigma weight residual 121.80 115.35 6.45 2.16e+00 2.14e-01 8.93e+00 angle pdb=" C SER F 197 " pdb=" N ARG F 198 " pdb=" CA ARG F 198 " ideal model delta sigma weight residual 122.11 117.72 4.39 1.64e+00 3.72e-01 7.16e+00 ... (remaining 6114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2317 16.88 - 33.75: 278 33.75 - 50.63: 83 50.63 - 67.51: 17 67.51 - 84.38: 2 Dihedral angle restraints: 2697 sinusoidal: 1080 harmonic: 1617 Sorted by residual: dihedral pdb=" CA ARG F 198 " pdb=" C ARG F 198 " pdb=" N GLY F 199 " pdb=" CA GLY F 199 " ideal model delta harmonic sigma weight residual 180.00 147.70 32.30 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA LEU F 294 " pdb=" C LEU F 294 " pdb=" N ASN F 295 " pdb=" CA ASN F 295 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER F 329 " pdb=" C SER F 329 " pdb=" N LEU F 330 " pdb=" CA LEU F 330 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 393 0.033 - 0.066: 194 0.066 - 0.099: 53 0.099 - 0.132: 24 0.132 - 0.165: 1 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA PRO A 792 " pdb=" N PRO A 792 " pdb=" C PRO A 792 " pdb=" CB PRO A 792 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE A 809 " pdb=" N ILE A 809 " pdb=" C ILE A 809 " pdb=" CB ILE A 809 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO F 273 " pdb=" N PRO F 273 " pdb=" C PRO F 273 " pdb=" CB PRO F 273 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 662 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 197 " -0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C SER F 197 " 0.096 2.00e-02 2.50e+03 pdb=" O SER F 197 " -0.035 2.00e-02 2.50e+03 pdb=" N ARG F 198 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 204 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ARG F 204 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG F 204 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS F 205 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 200 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ALA F 200 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA F 200 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA F 201 " 0.010 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 577 2.75 - 3.29: 4159 3.29 - 3.82: 7966 3.82 - 4.36: 9931 4.36 - 4.90: 16178 Nonbonded interactions: 38811 Sorted by model distance: nonbonded pdb=" NH2 ARG F 422 " pdb=" O LEU F 445 " model vdw 2.210 3.120 nonbonded pdb=" OD2 ASP F 44 " pdb=" OH TYR F 127 " model vdw 2.270 3.040 nonbonded pdb=" O SER F 181 " pdb=" OG SER F 181 " model vdw 2.285 3.040 nonbonded pdb=" O SER F 274 " pdb=" OG SER F 274 " model vdw 2.295 3.040 nonbonded pdb=" OD2 ASP F 192 " pdb=" NH2 ARG F 239 " model vdw 2.303 3.120 ... (remaining 38806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.210 Find NCS groups from input model: 0.040 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.004 0.041 4528 Z= 0.291 Angle : 0.723 10.660 6119 Z= 0.408 Chirality : 0.043 0.165 665 Planarity : 0.005 0.056 800 Dihedral : 16.205 84.384 1659 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 18.06 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.80 (0.33), residues: 557 helix: -0.58 (0.35), residues: 169 sheet: 0.20 (0.44), residues: 116 loop : -0.72 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.005 0.002 HIS F 310 PHE 0.021 0.002 PHE F 43 TYR 0.013 0.002 TYR F 230 ARG 0.004 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.544 Fit side-chains REVERT: F 49 ASN cc_start: 0.8735 (m110) cc_final: 0.8491 (m-40) REVERT: F 50 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7785 (mtt90) REVERT: F 83 LYS cc_start: 0.8556 (mttp) cc_final: 0.8168 (mtpt) REVERT: F 170 GLN cc_start: 0.7913 (tt0) cc_final: 0.7681 (tt0) REVERT: F 397 ILE cc_start: 0.9065 (mm) cc_final: 0.8821 (mm) REVERT: F 453 PHE cc_start: 0.7531 (t80) cc_final: 0.7271 (m-10) REVERT: F 520 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8477 (mtpt) REVERT: A 830 GLU cc_start: 0.7558 (mp0) cc_final: 0.7291 (mp0) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.3168 time to fit residues: 126.8414 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS F 76 GLN F 106 ASN F 110 HIS F 123 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 281 GLN F 286 ASN F 295 ASN F 387 ASN F 487 HIS F 493 ASN F 512 HIS A 791 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4528 Z= 0.301 Angle : 0.637 9.717 6119 Z= 0.334 Chirality : 0.044 0.164 665 Planarity : 0.005 0.051 800 Dihedral : 5.467 30.380 612 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.80 % Allowed : 19.78 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.07 (0.35), residues: 557 helix: 0.45 (0.38), residues: 171 sheet: 0.66 (0.51), residues: 93 loop : -0.53 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 501 HIS 0.004 0.001 HIS F 374 PHE 0.023 0.002 PHE F 43 TYR 0.011 0.002 TYR F 7 ARG 0.003 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.560 Fit side-chains REVERT: F 49 ASN cc_start: 0.8947 (m110) cc_final: 0.8737 (m-40) REVERT: F 83 LYS cc_start: 0.8558 (mttp) cc_final: 0.8181 (mtpt) REVERT: F 116 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mmtm) REVERT: F 170 GLN cc_start: 0.7915 (tt0) cc_final: 0.7708 (tt0) REVERT: F 303 GLU cc_start: 0.8362 (tt0) cc_final: 0.7724 (tt0) REVERT: F 397 ILE cc_start: 0.9034 (mm) cc_final: 0.8806 (mm) REVERT: F 520 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8480 (mtpt) REVERT: A 782 ILE cc_start: 0.6699 (mt) cc_final: 0.6499 (mt) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 1.1757 time to fit residues: 98.9414 Evaluate side-chains 72 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4528 Z= 0.162 Angle : 0.543 9.522 6119 Z= 0.284 Chirality : 0.042 0.139 665 Planarity : 0.004 0.048 800 Dihedral : 4.865 33.166 609 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.80 % Allowed : 21.08 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.36 (0.35), residues: 557 helix: 1.10 (0.38), residues: 166 sheet: 0.63 (0.50), residues: 93 loop : -0.33 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 22 HIS 0.004 0.001 HIS F 14 PHE 0.020 0.001 PHE F 43 TYR 0.009 0.001 TYR F 480 ARG 0.005 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.535 Fit side-chains REVERT: F 83 LYS cc_start: 0.8608 (mttp) cc_final: 0.8227 (mtpt) REVERT: F 116 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8292 (mmtm) REVERT: F 170 GLN cc_start: 0.7917 (tt0) cc_final: 0.7706 (tt0) REVERT: F 303 GLU cc_start: 0.8058 (tt0) cc_final: 0.7563 (tt0) REVERT: F 397 ILE cc_start: 0.8982 (mm) cc_final: 0.8736 (mm) REVERT: F 520 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8508 (mtpt) outliers start: 13 outliers final: 3 residues processed: 86 average time/residue: 1.2814 time to fit residues: 114.1771 Evaluate side-chains 69 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN A 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4528 Z= 0.344 Angle : 0.602 9.613 6119 Z= 0.321 Chirality : 0.044 0.151 665 Planarity : 0.004 0.051 800 Dihedral : 5.192 34.323 609 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.15 % Allowed : 22.15 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.36 (0.35), residues: 557 helix: 1.04 (0.38), residues: 166 sheet: 0.43 (0.48), residues: 93 loop : -0.22 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 PHE 0.020 0.002 PHE F 43 TYR 0.012 0.002 TYR F 109 ARG 0.004 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.441 Fit side-chains REVERT: F 83 LYS cc_start: 0.8609 (mttp) cc_final: 0.8241 (mtpt) REVERT: F 116 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8351 (mmtm) REVERT: F 170 GLN cc_start: 0.7926 (tt0) cc_final: 0.7720 (tt0) REVERT: F 270 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: F 303 GLU cc_start: 0.8409 (tt0) cc_final: 0.7857 (tt0) REVERT: F 520 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8535 (mtpt) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 1.3608 time to fit residues: 103.5896 Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.023 4528 Z= 0.191 Angle : 0.536 9.540 6119 Z= 0.285 Chirality : 0.042 0.142 665 Planarity : 0.004 0.048 800 Dihedral : 4.856 35.330 609 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.72 % Allowed : 22.80 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.50 (0.35), residues: 557 helix: 1.32 (0.39), residues: 166 sheet: 0.45 (0.49), residues: 93 loop : -0.22 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 PHE 0.019 0.001 PHE F 43 TYR 0.008 0.001 TYR F 480 ARG 0.004 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.790 Fit side-chains REVERT: F 83 LYS cc_start: 0.8610 (mttp) cc_final: 0.8232 (mtpt) REVERT: F 116 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: F 170 GLN cc_start: 0.7913 (tt0) cc_final: 0.7703 (tt0) REVERT: F 303 GLU cc_start: 0.8174 (tt0) cc_final: 0.7670 (tt0) REVERT: F 520 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8536 (mtpt) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 1.2941 time to fit residues: 94.5335 Evaluate side-chains 64 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 72 GLN ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4528 Z= 0.163 Angle : 0.521 9.424 6119 Z= 0.275 Chirality : 0.042 0.136 665 Planarity : 0.004 0.047 800 Dihedral : 4.667 35.623 609 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 23.44 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.35), residues: 557 helix: 1.58 (0.39), residues: 166 sheet: 0.47 (0.49), residues: 91 loop : -0.18 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 416 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.009 0.001 TYR F 480 ARG 0.004 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.524 Fit side-chains REVERT: F 14 HIS cc_start: 0.6746 (t-170) cc_final: 0.6529 (t70) REVERT: F 83 LYS cc_start: 0.8620 (mttp) cc_final: 0.8237 (mtpt) REVERT: F 116 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8266 (mmtm) REVERT: F 170 GLN cc_start: 0.7920 (tt0) cc_final: 0.7707 (tt0) REVERT: F 270 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: F 303 GLU cc_start: 0.8076 (tt0) cc_final: 0.7656 (tt0) REVERT: F 520 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8534 (mtpt) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 1.4017 time to fit residues: 104.4491 Evaluate side-chains 68 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4528 Z= 0.161 Angle : 0.514 9.430 6119 Z= 0.274 Chirality : 0.041 0.133 665 Planarity : 0.004 0.047 800 Dihedral : 4.598 35.485 609 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.37 % Allowed : 23.44 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.66 (0.35), residues: 557 helix: 1.74 (0.39), residues: 166 sheet: 0.09 (0.46), residues: 111 loop : -0.13 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 PHE 0.017 0.001 PHE F 43 TYR 0.008 0.001 TYR F 480 ARG 0.003 0.000 ARG F 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.493 Fit side-chains REVERT: F 14 HIS cc_start: 0.6778 (t-170) cc_final: 0.6552 (t70) REVERT: F 83 LYS cc_start: 0.8624 (mttp) cc_final: 0.8239 (mtpt) REVERT: F 116 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8276 (mmtm) REVERT: F 170 GLN cc_start: 0.7930 (tt0) cc_final: 0.7706 (tt0) REVERT: F 270 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: F 303 GLU cc_start: 0.8039 (tt0) cc_final: 0.7641 (tt0) REVERT: F 520 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8501 (mtpt) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 1.3385 time to fit residues: 97.0394 Evaluate side-chains 73 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4528 Z= 0.174 Angle : 0.515 9.392 6119 Z= 0.276 Chirality : 0.041 0.136 665 Planarity : 0.004 0.047 800 Dihedral : 4.612 35.432 609 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 24.09 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.67 (0.35), residues: 557 helix: 1.80 (0.39), residues: 166 sheet: 0.08 (0.45), residues: 111 loop : -0.15 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 416 HIS 0.004 0.001 HIS F 14 PHE 0.019 0.001 PHE F 43 TYR 0.008 0.001 TYR F 480 ARG 0.007 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: F 83 LYS cc_start: 0.8624 (mttp) cc_final: 0.8243 (mtpt) REVERT: F 116 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8282 (mmtm) REVERT: F 170 GLN cc_start: 0.7937 (tt0) cc_final: 0.7707 (tt0) REVERT: F 397 ILE cc_start: 0.8899 (mm) cc_final: 0.8676 (mm) REVERT: F 472 GLN cc_start: 0.8261 (tp40) cc_final: 0.8051 (tp40) REVERT: F 520 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8513 (mtpt) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 1.3396 time to fit residues: 94.2963 Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4528 Z= 0.207 Angle : 0.526 9.453 6119 Z= 0.283 Chirality : 0.042 0.137 665 Planarity : 0.004 0.048 800 Dihedral : 4.716 35.529 609 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 24.73 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.62 (0.35), residues: 557 helix: 1.73 (0.39), residues: 166 sheet: -0.02 (0.46), residues: 115 loop : -0.13 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 416 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.010 0.001 TYR F 109 ARG 0.007 0.000 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: F 14 HIS cc_start: 0.6723 (t-170) cc_final: 0.6508 (t70) REVERT: F 83 LYS cc_start: 0.8621 (mttp) cc_final: 0.8242 (mtpt) REVERT: F 116 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8285 (mmtm) REVERT: F 170 GLN cc_start: 0.7934 (tt0) cc_final: 0.7717 (tt0) REVERT: F 183 ASP cc_start: 0.7837 (t0) cc_final: 0.7559 (t0) REVERT: F 397 ILE cc_start: 0.8909 (mm) cc_final: 0.8680 (mm) REVERT: F 472 GLN cc_start: 0.8228 (tp40) cc_final: 0.8024 (tp40) REVERT: F 520 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8498 (mtpt) REVERT: A 830 GLU cc_start: 0.7486 (mp0) cc_final: 0.7243 (mp0) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 1.3208 time to fit residues: 93.1008 Evaluate side-chains 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4528 Z= 0.207 Angle : 0.534 9.457 6119 Z= 0.283 Chirality : 0.042 0.138 665 Planarity : 0.004 0.048 800 Dihedral : 4.720 35.500 609 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 24.09 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.66 (0.35), residues: 557 helix: 1.73 (0.39), residues: 166 sheet: 0.38 (0.50), residues: 94 loop : -0.24 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 416 HIS 0.005 0.001 HIS F 14 PHE 0.018 0.001 PHE F 43 TYR 0.009 0.001 TYR F 109 ARG 0.007 0.000 ARG F 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: F 83 LYS cc_start: 0.8620 (mttp) cc_final: 0.8242 (mtpt) REVERT: F 116 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8279 (mmtm) REVERT: F 170 GLN cc_start: 0.7931 (tt0) cc_final: 0.7710 (tt0) REVERT: F 183 ASP cc_start: 0.7801 (t0) cc_final: 0.7530 (t0) REVERT: F 397 ILE cc_start: 0.8903 (mm) cc_final: 0.8678 (mm) REVERT: F 520 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8499 (mtpt) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 1.3060 time to fit residues: 92.1892 Evaluate side-chains 71 residues out of total 474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 449 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098298 restraints weight = 5406.014| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.66 r_work: 0.3159 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4528 Z= 0.282 Angle : 0.557 9.504 6119 Z= 0.300 Chirality : 0.043 0.145 665 Planarity : 0.004 0.050 800 Dihedral : 4.907 35.464 609 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.72 % Allowed : 23.87 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.50 (0.35), residues: 557 helix: 1.58 (0.38), residues: 166 sheet: -0.11 (0.48), residues: 108 loop : -0.16 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 416 HIS 0.007 0.001 HIS F 14 PHE 0.017 0.001 PHE F 43 TYR 0.013 0.002 TYR F 109 ARG 0.007 0.000 ARG F 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.53 seconds wall clock time: 41 minutes 48.72 seconds (2508.72 seconds total)