Starting phenix.real_space_refine on Fri Dec 27 09:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xor_33357/12_2024/7xor_33357.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xor_33357/12_2024/7xor_33357.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/7xor_33357/12_2024/7xor_33357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xor_33357/12_2024/7xor_33357.map" model { file = "/net/cci-nas-00/data/ceres_data/7xor_33357/12_2024/7xor_33357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xor_33357/12_2024/7xor_33357.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 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.12, per 1000 atoms: 0.81 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 87, 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: 0.99 Conformation dependent library (CDL) restraints added in 519.6 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: 19 helices and 7 sheets defined 59.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.129A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.709A 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 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.590A pdb=" N PHE K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.529A pdb=" N LEU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.541A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 375 removed outlier: 3.932A 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: 4.075A 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 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 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: 3.541A pdb=" N ALA K 377 " --> pdb=" O VAL K 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.289A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE K 249 " --> 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 479 268 hydrogen bonds defined for protein. 771 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: 1.15 Time building geometry restraints manager: 1.15 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: 576 1.46 - 1.58: 1930 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CG GLU K 354 " pdb=" CD GLU K 354 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CD GLU K 354 " pdb=" OE1 GLU K 354 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 9.55e-01 bond pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.19e-02 7.06e+03 8.10e-01 bond pdb=" CA GLU K 355 " pdb=" CB GLU K 355 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.51e-02 4.39e+03 6.06e-01 bond pdb=" CG1 ILE K 150 " pdb=" CD1 ILE K 150 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.06e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 5038 1.10 - 2.20: 158 2.20 - 3.30: 28 3.30 - 4.40: 15 4.40 - 5.50: 4 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLU K 354 " pdb=" CA GLU K 354 " pdb=" CB GLU K 354 " ideal model delta sigma weight residual 110.01 115.51 -5.50 1.45e+00 4.76e-01 1.44e+01 angle pdb=" C GLU K 354 " pdb=" N GLU K 355 " pdb=" CA GLU K 355 " ideal model delta sigma weight residual 122.65 117.51 5.14 1.66e+00 3.63e-01 9.60e+00 angle pdb=" C ILE K 353 " pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 120.44 116.71 3.73 1.30e+00 5.92e-01 8.21e+00 angle pdb=" N GLY K 486 " pdb=" CA GLY K 486 " pdb=" C GLY K 486 " ideal model delta sigma weight residual 110.46 113.83 -3.37 1.43e+00 4.89e-01 5.57e+00 angle pdb=" N ALA K 449 " pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 112.75 115.77 -3.02 1.36e+00 5.41e-01 4.94e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2239 17.98 - 35.97: 142 35.97 - 53.95: 21 53.95 - 71.93: 6 71.93 - 89.92: 4 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CB GLU K 102 " pdb=" CG GLU K 102 " pdb=" CD GLU K 102 " pdb=" OE1 GLU K 102 " ideal model delta sinusoidal sigma weight residual 0.00 89.92 -89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB MET K 114 " pdb=" CG MET K 114 " pdb=" SD MET K 114 " pdb=" CE MET K 114 " ideal model delta sinusoidal sigma weight residual 60.00 119.85 -59.85 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU K 355 " pdb=" C GLU K 355 " pdb=" N ALA K 356 " pdb=" CA ALA K 356 " ideal model delta harmonic sigma weight residual 180.00 165.55 14.45 0 5.00e+00 4.00e-02 8.35e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 389 0.030 - 0.059: 166 0.059 - 0.089: 53 0.089 - 0.118: 27 0.118 - 0.148: 3 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU K 355 " pdb=" N GLU K 355 " pdb=" C GLU K 355 " pdb=" CB GLU K 355 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA GLU K 354 " pdb=" N GLU K 354 " pdb=" C GLU K 354 " pdb=" CB GLU K 354 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL K 136 " pdb=" N VAL K 136 " pdb=" C VAL K 136 " pdb=" CB VAL K 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 461 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO K 462 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO K 462 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 462 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 351 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C GLN K 351 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN K 351 " 0.008 2.00e-02 2.50e+03 pdb=" N GLN K 352 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 234 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO K 235 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO K 235 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 235 " -0.014 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 937 2.80 - 3.32: 4004 3.32 - 3.85: 6367 3.85 - 4.37: 7060 4.37 - 4.90: 12442 Nonbonded interactions: 30810 Sorted by model distance: nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP K 155 " pdb=" NH2 ARG K 395 " model vdw 2.293 3.120 nonbonded pdb=" OD1 ASP K 291 " pdb=" NH2 ARG K 345 " model vdw 2.306 3.120 nonbonded pdb=" OD1 ASP K 359 " pdb=" NH2 ARG K 362 " model vdw 2.351 3.120 nonbonded pdb=" OD1 ASN K 206 " pdb=" NZ LYS K 272 " model vdw 2.359 3.120 ... (remaining 30805 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: 1.750 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: 0.040 Process input model: 14.130 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: 19.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.030 3883 Z= 0.188 Angle : 0.519 5.499 5243 Z= 0.296 Chirality : 0.040 0.148 638 Planarity : 0.003 0.036 687 Dihedral : 12.604 89.918 1464 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 2.15 (0.36), residues: 522 helix: 2.32 (0.29), residues: 294 sheet: 1.40 (0.61), residues: 72 loop : -0.32 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.008 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.002 0.000 ARG K 268 *********************** 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 48 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5421 (tmtt) cc_final: 0.5115 (tmtt) REVERT: K 393 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8547 (ttpp) REVERT: K 491 MET cc_start: 0.8914 (mtm) cc_final: 0.8659 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1926 time to fit residues: 11.4330 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3883 Z= 0.164 Angle : 0.507 6.099 5243 Z= 0.276 Chirality : 0.040 0.136 638 Planarity : 0.003 0.041 687 Dihedral : 3.545 13.920 552 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.08 % 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: 2.24 (0.36), residues: 522 helix: 2.36 (0.28), residues: 301 sheet: 1.16 (0.60), residues: 72 loop : -0.16 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.017 0.001 PHE K 195 TYR 0.007 0.001 TYR K 360 ARG 0.003 0.000 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 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5243 (tmtt) cc_final: 0.4743 (tttm) REVERT: K 267 MET cc_start: 0.8400 (mmt) cc_final: 0.7783 (mtm) REVERT: K 352 GLN cc_start: 0.8812 (mt0) cc_final: 0.8364 (mt0) REVERT: K 388 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7763 (tp30) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1579 time to fit residues: 7.7645 Evaluate side-chains 31 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.0010 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3883 Z= 0.171 Angle : 0.463 6.791 5243 Z= 0.251 Chirality : 0.040 0.130 638 Planarity : 0.003 0.028 687 Dihedral : 3.550 15.445 552 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 8.42 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.36), residues: 522 helix: 2.44 (0.28), residues: 301 sheet: 1.11 (0.60), residues: 72 loop : -0.16 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.015 0.001 PHE K 195 TYR 0.007 0.001 TYR K 360 ARG 0.002 0.000 ARG K 322 *********************** 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 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5225 (tmtt) cc_final: 0.4644 (tttm) REVERT: K 352 GLN cc_start: 0.8818 (mt0) cc_final: 0.8413 (mt0) REVERT: K 366 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: K 388 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7803 (tp30) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.1608 time to fit residues: 8.0657 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3883 Z= 0.323 Angle : 0.529 5.277 5243 Z= 0.286 Chirality : 0.042 0.126 638 Planarity : 0.003 0.026 687 Dihedral : 3.716 15.971 552 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.23 % Allowed : 10.40 % Favored : 87.38 % 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: 1.98 (0.35), residues: 522 helix: 2.21 (0.28), residues: 302 sheet: 0.98 (0.60), residues: 72 loop : -0.40 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.013 0.001 PHE K 195 TYR 0.008 0.001 TYR K 476 ARG 0.003 0.000 ARG K 322 *********************** 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 43 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5232 (tmtt) cc_final: 0.4645 (tttm) REVERT: K 352 GLN cc_start: 0.8787 (mt0) cc_final: 0.8505 (mt0) REVERT: K 366 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: K 388 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7854 (tp30) REVERT: K 393 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8347 (ttmt) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.1734 time to fit residues: 8.5228 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 393 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3883 Z= 0.308 Angle : 0.511 7.532 5243 Z= 0.276 Chirality : 0.042 0.131 638 Planarity : 0.003 0.024 687 Dihedral : 3.766 15.895 552 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.72 % Allowed : 10.89 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.35), residues: 522 helix: 2.12 (0.28), residues: 302 sheet: 0.88 (0.60), residues: 72 loop : -0.42 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.014 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.002 0.000 ARG K 322 *********************** 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 45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5140 (tmtt) cc_final: 0.4616 (tttm) REVERT: K 146 GLN cc_start: 0.8752 (tp40) cc_final: 0.8461 (tp40) REVERT: K 348 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7461 (tm-30) REVERT: K 352 GLN cc_start: 0.8847 (mt0) cc_final: 0.8386 (mt0) REVERT: K 366 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: K 388 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7860 (tp30) outliers start: 11 outliers final: 5 residues processed: 41 average time/residue: 0.1581 time to fit residues: 8.6354 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 366 GLN Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3883 Z= 0.194 Angle : 0.463 6.185 5243 Z= 0.251 Chirality : 0.041 0.133 638 Planarity : 0.003 0.026 687 Dihedral : 3.703 16.045 552 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.99 (0.36), residues: 522 helix: 2.25 (0.29), residues: 299 sheet: 0.84 (0.60), residues: 72 loop : -0.32 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.014 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.002 0.000 ARG K 322 *********************** 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 44 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 16 MET cc_start: 0.8702 (mtm) cc_final: 0.8474 (mtp) REVERT: K 105 LYS cc_start: 0.5181 (tmtt) cc_final: 0.4628 (tttm) REVERT: K 146 GLN cc_start: 0.8735 (tp40) cc_final: 0.8448 (tp40) REVERT: K 267 MET cc_start: 0.8402 (mmt) cc_final: 0.7893 (mtp) REVERT: K 388 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7834 (tp30) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1626 time to fit residues: 8.7865 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3883 Z= 0.239 Angle : 0.497 6.403 5243 Z= 0.269 Chirality : 0.041 0.132 638 Planarity : 0.003 0.025 687 Dihedral : 3.706 16.146 552 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.73 % Allowed : 13.12 % Favored : 85.15 % 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: 1.97 (0.35), residues: 522 helix: 2.23 (0.28), residues: 299 sheet: 0.89 (0.60), residues: 72 loop : -0.34 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.012 0.001 PHE K 195 TYR 0.007 0.001 TYR K 476 ARG 0.003 0.000 ARG K 362 *********************** 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: 7 poor density : 33 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: K 105 LYS cc_start: 0.5208 (tmtt) cc_final: 0.4659 (tttm) REVERT: K 146 GLN cc_start: 0.8739 (tp40) cc_final: 0.8449 (tp40) REVERT: K 267 MET cc_start: 0.8422 (mmt) cc_final: 0.7892 (mtp) REVERT: K 352 GLN cc_start: 0.8803 (mt0) cc_final: 0.8403 (mt0) REVERT: K 388 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7826 (tp30) REVERT: K 518 GLU cc_start: 0.5231 (OUTLIER) cc_final: 0.4902 (mt-10) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1483 time to fit residues: 7.3985 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 354 GLU Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 491 MET Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3883 Z= 0.297 Angle : 0.514 6.465 5243 Z= 0.279 Chirality : 0.042 0.144 638 Planarity : 0.003 0.024 687 Dihedral : 3.771 16.335 552 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.73 % Allowed : 13.37 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.35), residues: 522 helix: 2.09 (0.28), residues: 302 sheet: 0.95 (0.61), residues: 72 loop : -0.39 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.012 0.001 PHE K 195 TYR 0.006 0.001 TYR K 360 ARG 0.002 0.000 ARG K 322 *********************** 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 41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.431 Fit side-chains REVERT: K 105 LYS cc_start: 0.5219 (tmtt) cc_final: 0.4708 (tttm) REVERT: K 138 CYS cc_start: 0.8626 (t) cc_final: 0.8365 (t) REVERT: K 146 GLN cc_start: 0.8753 (tp40) cc_final: 0.8452 (tp40) REVERT: K 267 MET cc_start: 0.8409 (mmt) cc_final: 0.7936 (mtp) REVERT: K 352 GLN cc_start: 0.8781 (mt0) cc_final: 0.8377 (mt0) REVERT: K 388 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7855 (tp30) REVERT: K 518 GLU cc_start: 0.5113 (OUTLIER) cc_final: 0.4774 (mt-10) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1476 time to fit residues: 7.3739 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 491 MET Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3883 Z= 0.313 Angle : 0.548 7.574 5243 Z= 0.300 Chirality : 0.042 0.172 638 Planarity : 0.003 0.024 687 Dihedral : 3.793 16.150 552 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.23 % Allowed : 12.87 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.35), residues: 522 helix: 2.03 (0.28), residues: 302 sheet: 0.94 (0.61), residues: 72 loop : -0.43 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.012 0.001 PHE K 195 TYR 0.006 0.001 TYR K 476 ARG 0.002 0.000 ARG K 322 *********************** 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 43 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.491 Fit side-chains REVERT: K 105 LYS cc_start: 0.5224 (tmtt) cc_final: 0.4709 (tttm) REVERT: K 138 CYS cc_start: 0.8616 (t) cc_final: 0.8355 (t) REVERT: K 146 GLN cc_start: 0.8754 (tp40) cc_final: 0.8439 (tp40) REVERT: K 267 MET cc_start: 0.8429 (mmt) cc_final: 0.7953 (mtp) REVERT: K 352 GLN cc_start: 0.8813 (mt0) cc_final: 0.8414 (mt0) REVERT: K 388 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7843 (tp30) REVERT: K 518 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4802 (mt-10) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.1394 time to fit residues: 7.2592 Evaluate side-chains 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3883 Z= 0.263 Angle : 0.534 7.395 5243 Z= 0.291 Chirality : 0.042 0.158 638 Planarity : 0.003 0.025 687 Dihedral : 3.762 15.442 552 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.73 % Allowed : 12.87 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.35), residues: 522 helix: 2.09 (0.28), residues: 299 sheet: 0.96 (0.61), residues: 72 loop : -0.39 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.013 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.002 0.000 ARG K 322 ********************** 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 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.539 Fit side-chains REVERT: K 105 LYS cc_start: 0.5220 (tmtt) cc_final: 0.4685 (tttm) REVERT: K 138 CYS cc_start: 0.8617 (t) cc_final: 0.8360 (t) REVERT: K 146 GLN cc_start: 0.8722 (tp40) cc_final: 0.8416 (tp40) REVERT: K 267 MET cc_start: 0.8414 (mmt) cc_final: 0.7983 (mtp) REVERT: K 352 GLN cc_start: 0.8805 (mt0) cc_final: 0.8430 (mt0) REVERT: K 388 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7820 (tp30) REVERT: K 518 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4754 (mt-10) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.1665 time to fit residues: 8.5498 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain K residue 360 TYR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain K residue 518 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.076649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063754 restraints weight = 11923.223| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.95 r_work: 0.3021 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3883 Z= 0.206 Angle : 0.521 7.380 5243 Z= 0.281 Chirality : 0.041 0.155 638 Planarity : 0.003 0.026 687 Dihedral : 3.714 14.849 552 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.49 % Allowed : 13.61 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.36), residues: 522 helix: 2.14 (0.28), residues: 299 sheet: 0.95 (0.61), residues: 72 loop : -0.40 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.013 0.001 PHE K 195 TYR 0.006 0.001 TYR K 360 ARG 0.002 0.000 ARG K 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1037.81 seconds wall clock time: 20 minutes 44.47 seconds (1244.47 seconds total)