Starting phenix.real_space_refine on Wed Mar 5 22:26:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoq_33356/03_2025/7xoq_33356.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoq_33356/03_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_33356/03_2025/7xoq_33356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2025/7xoq_33356.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_2025/7xoq_33356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoq_33356/03_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-5624/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: 2.91, per 1000 atoms: 0.75 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: 0.96 Conformation dependent library (CDL) restraints added in 530.3 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: 0.44 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: 1.11 Time building geometry restraints manager: 1.14 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- 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 : 0.411 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: 0.1961 time to fit residues: 10.1813 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 = 0.3366 r_free = 0.3366 target = 0.074427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063410 restraints weight = 11242.693| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.91 r_work: 0.2991 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.469 Fit side-chains REVERT: K 16 MET cc_start: 0.8014 (mtp) cc_final: 0.7715 (mtt) REVERT: K 334 ASP cc_start: 0.8241 (t0) cc_final: 0.7950 (t0) REVERT: K 514 MET cc_start: 0.8649 (mmm) cc_final: 0.8283 (mmm) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1532 time to fit residues: 7.0099 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 : 0.439 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.073671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062568 restraints weight = 11311.766| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.89 r_work: 0.2968 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3883 Z= 0.371 Angle : 0.570 6.173 5243 Z= 0.300 Chirality : 0.043 0.150 638 Planarity : 0.003 0.023 687 Dihedral : 4.121 17.564 552 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.04 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: 1.93 (0.37), residues: 522 helix: 2.35 (0.30), residues: 294 sheet: -0.16 (0.56), residues: 77 loop : -0.01 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 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 : 0.447 Fit side-chains REVERT: K 16 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7838 (mtt) REVERT: K 307 MET cc_start: 0.8457 (ptt) cc_final: 0.8239 (pmm) REVERT: K 334 ASP cc_start: 0.8205 (t0) cc_final: 0.7852 (t0) REVERT: K 514 MET cc_start: 0.8584 (mmm) cc_final: 0.8215 (mmm) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 0.1535 time to fit residues: 7.4474 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 : 0.431 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 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: 2.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.074737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063949 restraints weight = 11239.319| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.88 r_work: 0.3007 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1756 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= 0.211 Angle : 0.494 6.660 5243 Z= 0.259 Chirality : 0.041 0.141 638 Planarity : 0.003 0.020 687 Dihedral : 3.948 16.550 552 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.98 % Allowed : 12.13 % Favored : 85.89 % 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: 2.60 (0.30), residues: 297 sheet: -0.27 (0.56), residues: 77 loop : 0.01 (0.55), 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 0.002 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 : 0.378 Fit side-chains revert: symmetry clash REVERT: K 307 MET cc_start: 0.8477 (ptt) cc_final: 0.8244 (pmm) REVERT: K 334 ASP cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1418 time to fit residues: 6.9197 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 : 0.447 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.0870 overall best weight: 1.2762 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.076179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065349 restraints weight = 11490.348| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.94 r_work: 0.3038 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3883 Z= 0.149 Angle : 0.466 7.104 5243 Z= 0.245 Chirality : 0.040 0.140 638 Planarity : 0.002 0.019 687 Dihedral : 3.776 15.364 552 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 2.31 (0.38), residues: 522 helix: 2.80 (0.30), residues: 299 sheet: -0.30 (0.57), residues: 77 loop : -0.12 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 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 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 to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.397 Fit side-chains REVERT: K 307 MET cc_start: 0.8482 (ptt) cc_final: 0.8222 (pmm) REVERT: K 311 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8081 (mptt) REVERT: K 334 ASP cc_start: 0.8172 (t0) cc_final: 0.7855 (t0) REVERT: K 433 ASN cc_start: 0.8279 (t0) cc_final: 0.7999 (t0) REVERT: K 520 MET cc_start: 0.8438 (mmm) cc_final: 0.8230 (mtt) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1375 time to fit residues: 6.9620 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 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 = 0.3378 r_free = 0.3378 target = 0.075012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064195 restraints weight = 11246.756| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.88 r_work: 0.3014 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1872 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= 0.229 Angle : 0.491 6.888 5243 Z= 0.257 Chirality : 0.041 0.139 638 Planarity : 0.002 0.018 687 Dihedral : 3.798 16.288 552 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.72 % Allowed : 13.61 % Favored : 83.66 % 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: 2.26 (0.38), residues: 522 helix: 2.74 (0.30), residues: 298 sheet: -0.37 (0.57), residues: 77 loop : -0.03 (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 0.001 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 41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: K 307 MET cc_start: 0.8531 (ptt) cc_final: 0.8219 (pmm) REVERT: K 334 ASP cc_start: 0.8154 (t0) cc_final: 0.7856 (t0) REVERT: K 520 MET cc_start: 0.8610 (mmm) cc_final: 0.8408 (mtt) outliers start: 11 outliers final: 8 residues processed: 40 average time/residue: 0.1373 time to fit residues: 7.4574 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 : 0.437 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.076144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.065388 restraints weight = 11325.890| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.89 r_work: 0.3043 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3883 Z= 0.152 Angle : 0.474 7.330 5243 Z= 0.247 Chirality : 0.040 0.138 638 Planarity : 0.002 0.018 687 Dihedral : 3.714 15.361 552 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 2.37 (0.38), residues: 522 helix: 2.87 (0.30), residues: 299 sheet: -0.36 (0.57), residues: 77 loop : -0.09 (0.54), residues: 146 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: K 307 MET cc_start: 0.8606 (ptt) cc_final: 0.8230 (pmm) REVERT: K 334 ASP cc_start: 0.8151 (t0) cc_final: 0.7824 (t0) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.1487 time to fit residues: 7.7477 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 : 0.446 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.075518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064411 restraints weight = 11416.165| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.98 r_work: 0.3017 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1948 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= 0.216 Angle : 0.498 6.979 5243 Z= 0.257 Chirality : 0.041 0.134 638 Planarity : 0.002 0.018 687 Dihedral : 3.758 15.660 552 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 2.35 (0.38), residues: 522 helix: 2.84 (0.30), residues: 298 sheet: -0.44 (0.57), residues: 77 loop : 0.01 (0.54), residues: 147 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 0.002 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 : 0.454 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8200 (t0) cc_final: 0.7841 (t0) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1399 time to fit residues: 7.2974 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 : 0.479 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 0.0570 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.075165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064288 restraints weight = 11448.876| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.92 r_work: 0.3017 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1974 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= 0.217 Angle : 0.503 6.972 5243 Z= 0.259 Chirality : 0.041 0.133 638 Planarity : 0.002 0.018 687 Dihedral : 3.786 15.754 552 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 2.32 (0.38), residues: 522 helix: 2.81 (0.30), residues: 298 sheet: -0.47 (0.57), residues: 77 loop : 0.01 (0.54), residues: 147 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 0.007 0.001 TYR K 478 ARG 0.001 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 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8165 (t0) cc_final: 0.7827 (t0) outliers start: 9 outliers final: 9 residues processed: 38 average time/residue: 0.1400 time to fit residues: 7.2065 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 : 0.454 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.076216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065274 restraints weight = 11341.249| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.93 r_work: 0.3040 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2020 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= 0.157 Angle : 0.487 7.420 5243 Z= 0.250 Chirality : 0.040 0.135 638 Planarity : 0.002 0.019 687 Dihedral : 3.723 15.066 552 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.48 % Allowed : 14.60 % 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: 2.43 (0.38), residues: 522 helix: 2.92 (0.29), residues: 298 sheet: -0.40 (0.58), residues: 77 loop : 0.01 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.007 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: K 334 ASP cc_start: 0.8108 (t0) cc_final: 0.7779 (t0) REVERT: K 514 MET cc_start: 0.8548 (mmm) cc_final: 0.8296 (mmm) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1399 time to fit residues: 7.2292 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 : 0.443 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.077662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.066923 restraints weight = 11110.387| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.89 r_work: 0.3084 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2091 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 : 0.483 7.893 5243 Z= 0.249 Chirality : 0.040 0.138 638 Planarity : 0.002 0.019 687 Dihedral : 3.685 14.427 552 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 15.35 % 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: 2.44 (0.38), residues: 522 helix: 2.92 (0.29), residues: 298 sheet: -0.34 (0.58), residues: 77 loop : -0.03 (0.53), residues: 147 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 0.007 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: 1696.88 seconds wall clock time: 30 minutes 18.50 seconds (1818.50 seconds total)