Starting phenix.real_space_refine on Sun Mar 10 18:15:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoq_33356/03_2024/7xoq_33356.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "K GLU 232": "OE1" <-> "OE2" Residue "K GLU 397": "OE1" <-> "OE2" Residue "K ASP 490": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 2.51, per 1000 atoms: 0.65 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 84.39, 70.47, 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 20 16.00 O 773 8.00 N 665 7.00 C 2397 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 - 3.50 Amino acid : False - 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: 1.53 Conformation dependent library (CDL) restraints added in 891.3 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 61.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.566A pdb=" N ARG K 13 " --> pdb=" O GLY K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.932A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 110 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.569A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.521A pdb=" N PHE K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 205' Processing helix chain 'K' and resid 229 through 244 removed outlier: 4.442A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 296 removed outlier: 3.534A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.438A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 459 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.550A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.515A pdb=" N THR K 522 " --> pdb=" O ASP K 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS K 7 " --> pdb=" O MET K 520 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179 removed outlier: 3.858A pdb=" N ASP K 188 " --> pdb=" O VAL K 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 192 through 193 removed outlier: 6.667A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 192 through 193 removed outlier: 6.667A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479 267 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1340 1.34 - 1.46: 564 1.46 - 1.58: 1942 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" SD MET K 520 " pdb=" CE MET K 520 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB ASP K 334 " pdb=" CG ASP K 334 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.70e-01 bond pdb=" CB MET K 16 " pdb=" CG MET K 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.25e-01 bond pdb=" CB MET K 520 " pdb=" CG MET K 520 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" N GLY K 477 " pdb=" CA GLY K 477 " ideal model delta sigma weight residual 1.443 1.452 -0.009 1.17e-02 7.31e+03 5.99e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.09: 74 106.09 - 112.35: 2061 112.35 - 118.60: 1129 118.60 - 124.86: 1964 124.86 - 131.11: 15 Bond angle restraints: 5243 Sorted by residual: angle pdb=" CB ARG K 197 " pdb=" CG ARG K 197 " pdb=" CD ARG K 197 " ideal model delta sigma weight residual 111.30 118.95 -7.65 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N SER K 139 " pdb=" CA SER K 139 " pdb=" C SER K 139 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N GLU K 354 " pdb=" CA GLU K 354 " pdb=" CB GLU K 354 " ideal model delta sigma weight residual 110.39 115.01 -4.62 1.75e+00 3.27e-01 6.96e+00 angle pdb=" CA LEU K 222 " pdb=" CB LEU K 222 " pdb=" CG LEU K 222 " ideal model delta sigma weight residual 116.30 124.31 -8.01 3.50e+00 8.16e-02 5.24e+00 angle pdb=" C ILE K 353 " pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 121.18 116.68 4.50 1.98e+00 2.55e-01 5.16e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 2210 15.45 - 30.90: 171 30.90 - 46.35: 25 46.35 - 61.79: 2 61.79 - 77.24: 4 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA ALA K 26 " pdb=" C ALA K 26 " pdb=" N VAL K 27 " pdb=" CA VAL K 27 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ARG K 197 " pdb=" C ARG K 197 " pdb=" N GLY K 198 " pdb=" CA GLY K 198 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLN K 97 " pdb=" CB GLN K 97 " pdb=" CG GLN K 97 " pdb=" CD GLN K 97 " ideal model delta sinusoidal sigma weight residual -60.00 -105.53 45.53 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 374 0.025 - 0.051: 150 0.051 - 0.076: 68 0.076 - 0.101: 30 0.101 - 0.127: 16 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL K 213 " pdb=" N VAL K 213 " pdb=" C VAL K 213 " pdb=" CB VAL K 213 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL K 412 " pdb=" N VAL K 412 " pdb=" C VAL K 412 " pdb=" CB VAL K 412 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE K 175 " pdb=" N ILE K 175 " pdb=" C ILE K 175 " pdb=" CB ILE K 175 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 334 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ASP K 334 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP K 334 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY K 335 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 197 " -0.090 9.50e-02 1.11e+02 4.06e-02 1.04e+00 pdb=" NE ARG K 197 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG K 197 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 197 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG K 197 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 201 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO K 202 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO K 202 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 202 " 0.012 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 947 2.80 - 3.33: 4000 3.33 - 3.85: 6383 3.85 - 4.38: 7071 4.38 - 4.90: 12435 Nonbonded interactions: 30836 Sorted by model distance: nonbonded pdb=" O GLU K 339 " pdb=" NE2 GLN K 343 " model vdw 2.277 2.520 nonbonded pdb=" OD2 ASP K 155 " pdb=" NH2 ARG K 395 " model vdw 2.297 2.520 nonbonded pdb=" O ARG K 421 " pdb=" OG SER K 424 " model vdw 2.308 2.440 nonbonded pdb=" NH1 ARG K 421 " pdb=" O GLY K 472 " model vdw 2.339 2.520 nonbonded pdb=" OD1 ASP K 291 " pdb=" NE ARG K 345 " model vdw 2.340 2.520 ... (remaining 30831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 5.830 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.280 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.003 0.027 3883 Z= 0.198 Angle : 0.543 8.011 5243 Z= 0.305 Chirality : 0.038 0.127 638 Planarity : 0.003 0.041 687 Dihedral : 11.307 77.243 1464 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.13 (0.37), residues: 522 helix: 2.50 (0.30), residues: 293 sheet: 0.35 (0.58), residues: 77 loop : -0.17 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.012 0.001 TYR K 199 ARG 0.003 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.459 Fit side-chains REVERT: K 268 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7162 (mmt180) REVERT: K 433 ASN cc_start: 0.8160 (t0) cc_final: 0.7613 (t0) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2057 time to fit residues: 10.6733 Evaluate side-chains 28 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 453 GLN K 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3883 Z= 0.276 Angle : 0.529 6.327 5243 Z= 0.276 Chirality : 0.041 0.141 638 Planarity : 0.003 0.022 687 Dihedral : 3.908 17.121 552 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.99 % Allowed : 6.44 % Favored : 92.57 % 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: 2.18 (0.37), residues: 522 helix: 2.51 (0.30), residues: 297 sheet: 0.32 (0.58), residues: 77 loop : -0.12 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.003 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.471 Fit side-chains REVERT: K 16 MET cc_start: 0.7553 (mtp) cc_final: 0.7185 (mtt) REVERT: K 334 ASP cc_start: 0.7799 (t0) cc_final: 0.7429 (t0) REVERT: K 433 ASN cc_start: 0.8043 (t0) cc_final: 0.7726 (t0) REVERT: K 514 MET cc_start: 0.8322 (mmm) cc_final: 0.7803 (mmm) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1576 time to fit residues: 7.3606 Evaluate side-chains 32 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3883 Z= 0.217 Angle : 0.483 6.763 5243 Z= 0.252 Chirality : 0.040 0.148 638 Planarity : 0.003 0.023 687 Dihedral : 3.812 16.522 552 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.49 % Allowed : 8.42 % Favored : 90.10 % 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: 2.29 (0.37), residues: 522 helix: 2.65 (0.30), residues: 297 sheet: 0.25 (0.57), residues: 77 loop : -0.13 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.007 0.001 TYR K 478 ARG 0.001 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.490 Fit side-chains REVERT: K 16 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7341 (mtt) REVERT: K 334 ASP cc_start: 0.7781 (t0) cc_final: 0.7333 (t0) REVERT: K 433 ASN cc_start: 0.8057 (t0) cc_final: 0.7496 (t0) REVERT: K 514 MET cc_start: 0.8186 (mmm) cc_final: 0.7688 (mmm) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.1510 time to fit residues: 7.1315 Evaluate side-chains 32 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 343 GLN ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3883 Z= 0.176 Angle : 0.466 7.149 5243 Z= 0.241 Chirality : 0.040 0.139 638 Planarity : 0.002 0.020 687 Dihedral : 3.709 15.891 552 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.48 % Allowed : 9.90 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.38), residues: 522 helix: 2.81 (0.30), residues: 297 sheet: 0.10 (0.57), residues: 77 loop : -0.13 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.001 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.459 Fit side-chains REVERT: K 311 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8130 (mptt) REVERT: K 334 ASP cc_start: 0.7730 (t0) cc_final: 0.7293 (t0) REVERT: K 433 ASN cc_start: 0.8070 (t0) cc_final: 0.7606 (t0) REVERT: K 514 MET cc_start: 0.8206 (mmm) cc_final: 0.7985 (mmm) outliers start: 10 outliers final: 4 residues processed: 39 average time/residue: 0.1421 time to fit residues: 7.4860 Evaluate side-chains 35 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3883 Z= 0.151 Angle : 0.454 7.134 5243 Z= 0.237 Chirality : 0.040 0.138 638 Planarity : 0.002 0.019 687 Dihedral : 3.649 15.615 552 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.73 % Allowed : 11.88 % Favored : 86.39 % 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: 2.44 (0.38), residues: 522 helix: 2.92 (0.30), residues: 297 sheet: 0.10 (0.58), residues: 72 loop : -0.28 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.007 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.001 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: K 233 MET cc_start: 0.8160 (mtm) cc_final: 0.7938 (mtm) REVERT: K 311 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8119 (mptt) REVERT: K 334 ASP cc_start: 0.7741 (t0) cc_final: 0.7336 (t0) REVERT: K 514 MET cc_start: 0.8090 (mmm) cc_final: 0.7692 (mmm) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1507 time to fit residues: 7.4845 Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3883 Z= 0.270 Angle : 0.501 6.670 5243 Z= 0.261 Chirality : 0.041 0.141 638 Planarity : 0.003 0.019 687 Dihedral : 3.758 16.463 552 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 12.87 % Favored : 85.40 % 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: 2.35 (0.38), residues: 522 helix: 2.81 (0.30), residues: 297 sheet: 0.15 (0.59), residues: 72 loop : -0.28 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.002 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: K 233 MET cc_start: 0.8234 (mtm) cc_final: 0.8021 (mtm) REVERT: K 334 ASP cc_start: 0.7760 (t0) cc_final: 0.7328 (t0) REVERT: K 514 MET cc_start: 0.8172 (mmm) cc_final: 0.7913 (mmm) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.1436 time to fit residues: 7.1897 Evaluate side-chains 35 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3883 Z= 0.124 Angle : 0.450 7.073 5243 Z= 0.234 Chirality : 0.039 0.136 638 Planarity : 0.002 0.019 687 Dihedral : 3.579 14.802 552 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 13.61 % Favored : 84.90 % 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: 2.56 (0.38), residues: 522 helix: 3.03 (0.30), residues: 297 sheet: 0.17 (0.61), residues: 72 loop : -0.27 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.007 0.001 TYR K 476 ARG 0.001 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: K 233 MET cc_start: 0.8184 (mtm) cc_final: 0.7959 (mtm) REVERT: K 311 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7824 (mtpp) REVERT: K 334 ASP cc_start: 0.7727 (t0) cc_final: 0.7308 (t0) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1497 time to fit residues: 7.4536 Evaluate side-chains 34 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3883 Z= 0.277 Angle : 0.510 6.690 5243 Z= 0.263 Chirality : 0.041 0.139 638 Planarity : 0.003 0.019 687 Dihedral : 3.714 16.164 552 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.98 % Allowed : 13.61 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.37), residues: 522 helix: 2.82 (0.29), residues: 297 sheet: 0.18 (0.59), residues: 72 loop : -0.28 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.002 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: K 233 MET cc_start: 0.8234 (mtm) cc_final: 0.8012 (mtm) REVERT: K 334 ASP cc_start: 0.7753 (t0) cc_final: 0.7320 (t0) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.1378 time to fit residues: 6.9750 Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 30 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3883 Z= 0.130 Angle : 0.462 7.026 5243 Z= 0.237 Chirality : 0.040 0.137 638 Planarity : 0.002 0.018 687 Dihedral : 3.604 14.983 552 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 13.61 % Favored : 84.90 % 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: 2.53 (0.38), residues: 522 helix: 2.99 (0.29), residues: 297 sheet: 0.17 (0.60), residues: 72 loop : -0.25 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.008 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.001 0.000 ARG K 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: K 311 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7996 (mtpp) REVERT: K 334 ASP cc_start: 0.7737 (t0) cc_final: 0.7307 (t0) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.1478 time to fit residues: 7.2269 Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3883 Z= 0.254 Angle : 0.516 7.585 5243 Z= 0.264 Chirality : 0.041 0.157 638 Planarity : 0.003 0.018 687 Dihedral : 3.714 15.913 552 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 13.61 % Favored : 84.65 % 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: 2.37 (0.37), residues: 522 helix: 2.82 (0.29), residues: 297 sheet: 0.12 (0.59), residues: 72 loop : -0.23 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.006 0.001 TYR K 199 ARG 0.002 0.000 ARG K 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.7747 (t0) cc_final: 0.7281 (t0) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1505 time to fit residues: 6.9873 Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 27 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.078120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067284 restraints weight = 11203.811| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.93 r_work: 0.3084 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3883 Z= 0.120 Angle : 0.475 7.584 5243 Z= 0.246 Chirality : 0.040 0.136 638 Planarity : 0.002 0.018 687 Dihedral : 3.619 14.614 552 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.49 % Allowed : 13.86 % Favored : 84.65 % 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: 2.53 (0.38), residues: 522 helix: 2.99 (0.30), residues: 297 sheet: 0.16 (0.60), residues: 72 loop : -0.24 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.007 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.001 0.000 ARG K 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1043.63 seconds wall clock time: 19 minutes 48.53 seconds (1188.53 seconds total)