Starting phenix.real_space_refine on Tue Feb 11 03:14:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_33356.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_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/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_33356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_33356.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_33356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoq_33356/02_2025/7xoq_33356.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.63, per 1000 atoms: 0.94 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 490.3 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: 1.38 Time building geometry restraints manager: 1.05 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: 0.00 - 1.60: 5145 1.60 - 3.20: 81 3.20 - 4.81: 12 4.81 - 6.41: 3 6.41 - 8.01: 2 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 3.120 nonbonded pdb=" OD2 ASP K 155 " pdb=" NH2 ARG K 395 " model vdw 2.297 3.120 nonbonded pdb=" O ARG K 421 " pdb=" OG SER K 424 " model vdw 2.308 3.040 nonbonded pdb=" NH1 ARG K 421 " pdb=" O GLY K 472 " model vdw 2.339 3.120 nonbonded pdb=" OD1 ASP K 291 " pdb=" NE ARG K 345 " model vdw 2.340 3.120 ... (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: 1.300 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.383 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: 0.2015 time to fit residues: 10.4755 Evaluate side-chains 28 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** K 453 GLN K 457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.074481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063431 restraints weight = 11265.426| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.92 r_work: 0.2990 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3883 Z= 0.342 Angle : 0.572 6.159 5243 Z= 0.301 Chirality : 0.043 0.145 638 Planarity : 0.003 0.021 687 Dihedral : 4.038 17.638 552 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.99 % Allowed : 5.94 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.37), residues: 522 helix: 2.45 (0.30), residues: 295 sheet: 0.16 (0.58), residues: 77 loop : -0.08 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 401 PHE 0.009 0.002 PHE K 195 TYR 0.009 0.001 TYR K 199 ARG 0.004 0.001 ARG K 421 *********************** 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 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.349 Fit side-chains REVERT: K 16 MET cc_start: 0.8011 (mtp) cc_final: 0.7716 (mtt) REVERT: K 334 ASP cc_start: 0.8237 (t0) cc_final: 0.7950 (t0) REVERT: K 514 MET cc_start: 0.8646 (mmm) cc_final: 0.8283 (mmm) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1414 time to fit residues: 6.4779 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 42 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063025 restraints weight = 11240.697| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.87 r_work: 0.2983 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3883 Z= 0.336 Angle : 0.548 6.263 5243 Z= 0.288 Chirality : 0.042 0.145 638 Planarity : 0.003 0.021 687 Dihedral : 4.057 17.370 552 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.23 % Allowed : 8.66 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.37), residues: 522 helix: 2.40 (0.30), residues: 296 sheet: -0.11 (0.56), residues: 77 loop : -0.04 (0.53), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.010 0.002 PHE K 195 TYR 0.007 0.001 TYR K 199 ARG 0.002 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 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.472 Fit side-chains REVERT: K 16 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7854 (mtt) REVERT: K 334 ASP cc_start: 0.8192 (t0) cc_final: 0.7842 (t0) REVERT: K 514 MET cc_start: 0.8557 (mmm) cc_final: 0.8183 (mmm) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1493 time to fit residues: 7.3717 Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 187 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063775 restraints weight = 11251.925| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.96 r_work: 0.2995 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.003 0.026 3883 Z= 0.230 Angle : 0.500 6.965 5243 Z= 0.262 Chirality : 0.041 0.139 638 Planarity : 0.003 0.020 687 Dihedral : 3.935 16.817 552 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.98 % Allowed : 12.38 % Favored : 85.64 % 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: 2.16 (0.38), residues: 522 helix: 2.58 (0.30), residues: 297 sheet: -0.20 (0.57), residues: 77 loop : -0.01 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.010 0.001 PHE K 195 TYR 0.007 0.001 TYR K 478 ARG 0.003 0.000 ARG K 421 *********************** 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 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8190 (t0) cc_final: 0.7847 (t0) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1523 time to fit residues: 7.4141 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 354 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064263 restraints weight = 11534.141| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.93 r_work: 0.3014 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3883 Z= 0.211 Angle : 0.489 6.861 5243 Z= 0.256 Chirality : 0.040 0.138 638 Planarity : 0.002 0.020 687 Dihedral : 3.883 16.443 552 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.98 % Allowed : 14.11 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.38), residues: 522 helix: 2.69 (0.30), residues: 298 sheet: -0.29 (0.56), residues: 77 loop : -0.07 (0.54), residues: 147 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 0.002 0.000 ARG K 421 *********************** 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 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8192 (t0) cc_final: 0.7853 (t0) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.1537 time to fit residues: 7.4425 Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063632 restraints weight = 11297.281| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.94 r_work: 0.2992 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3883 Z= 0.264 Angle : 0.509 6.721 5243 Z= 0.267 Chirality : 0.041 0.139 638 Planarity : 0.003 0.019 687 Dihedral : 3.906 16.575 552 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.23 % Allowed : 14.85 % Favored : 82.92 % 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: 2.17 (0.38), residues: 522 helix: 2.65 (0.30), residues: 297 sheet: -0.36 (0.57), residues: 77 loop : -0.03 (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 421 *********************** 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 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8228 (t0) cc_final: 0.7891 (t0) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1467 time to fit residues: 7.1777 Evaluate side-chains 35 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 38 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064657 restraints weight = 11354.775| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.91 r_work: 0.3023 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1891 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= 0.182 Angle : 0.476 6.912 5243 Z= 0.250 Chirality : 0.040 0.137 638 Planarity : 0.002 0.018 687 Dihedral : 3.784 15.852 552 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.98 % Allowed : 14.85 % Favored : 83.17 % 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: 2.28 (0.38), residues: 522 helix: 2.79 (0.30), residues: 298 sheet: -0.39 (0.56), residues: 77 loop : -0.08 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.010 0.001 PHE K 195 TYR 0.007 0.001 TYR K 476 ARG 0.002 0.000 ARG K 421 *********************** 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 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8195 (t0) cc_final: 0.7837 (t0) outliers start: 8 outliers final: 8 residues processed: 36 average time/residue: 0.1450 time to fit residues: 7.0420 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 89 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.075941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.064963 restraints weight = 11316.963| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.96 r_work: 0.3025 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.003 0.024 3883 Z= 0.176 Angle : 0.482 7.158 5243 Z= 0.249 Chirality : 0.040 0.137 638 Planarity : 0.002 0.019 687 Dihedral : 3.733 15.535 552 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.48 % Allowed : 14.85 % Favored : 82.67 % 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: 2.32 (0.38), residues: 522 helix: 2.81 (0.30), residues: 298 sheet: -0.39 (0.56), residues: 77 loop : -0.05 (0.53), residues: 147 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 476 ARG 0.001 0.000 ARG K 421 *********************** 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 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8205 (t0) cc_final: 0.7860 (t0) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1423 time to fit residues: 7.3000 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 VAL 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 378 VAL 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 3 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.0030 chunk 47 optimal weight: 3.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065332 restraints weight = 11370.600| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.92 r_work: 0.3040 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3883 Z= 0.156 Angle : 0.487 7.161 5243 Z= 0.249 Chirality : 0.040 0.137 638 Planarity : 0.002 0.019 687 Dihedral : 3.701 15.286 552 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.98 % Allowed : 15.35 % Favored : 82.67 % 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: 2.38 (0.38), residues: 522 helix: 2.87 (0.30), residues: 298 sheet: -0.38 (0.56), residues: 77 loop : -0.02 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.008 0.001 PHE K 195 TYR 0.007 0.001 TYR K 476 ARG 0.002 0.000 ARG K 421 *********************** 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 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: K 193 MET cc_start: 0.8792 (ttm) cc_final: 0.8574 (ttm) REVERT: K 334 ASP cc_start: 0.8183 (t0) cc_final: 0.7826 (t0) REVERT: K 514 MET cc_start: 0.8647 (mmm) cc_final: 0.8228 (mmm) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.1488 time to fit residues: 7.3974 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 330 THR Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 378 VAL 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 24 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065449 restraints weight = 11263.657| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.90 r_work: 0.3045 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3883 Z= 0.160 Angle : 0.486 7.510 5243 Z= 0.249 Chirality : 0.040 0.139 638 Planarity : 0.002 0.019 687 Dihedral : 3.680 15.108 552 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.23 % Allowed : 14.85 % Favored : 82.92 % 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: 2.39 (0.38), residues: 522 helix: 2.89 (0.29), residues: 298 sheet: -0.43 (0.56), residues: 77 loop : -0.00 (0.53), residues: 147 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 476 ARG 0.002 0.000 ARG K 421 ********************** 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 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: K 311 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7905 (mtpp) REVERT: K 334 ASP cc_start: 0.8142 (t0) cc_final: 0.7809 (t0) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.1482 time to fit residues: 7.6019 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 56 VAL 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 378 VAL 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 23 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 0.0770 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065612 restraints weight = 11171.066| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.96 r_work: 0.3047 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3883 Z= 0.168 Angle : 0.493 7.417 5243 Z= 0.256 Chirality : 0.040 0.140 638 Planarity : 0.002 0.019 687 Dihedral : 3.676 14.937 552 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.23 % Allowed : 14.60 % Favored : 83.17 % 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: 2.90 (0.30), residues: 298 sheet: -0.41 (0.56), residues: 77 loop : -0.04 (0.53), residues: 147 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 476 ARG 0.002 0.000 ARG K 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.69 seconds wall clock time: 31 minutes 51.79 seconds (1911.79 seconds total)