Starting phenix.real_space_refine on Sun Mar 10 18:13:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/03_2024/7xop_33355.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 102": "OE1" <-> "OE2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 291": "OD1" <-> "OD2" Residue "K ASP 361": "OD1" <-> "OD2" Residue "K ASP 473": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 2.49, per 1000 atoms: 0.65 Number of scatterers: 3855 At special positions: 0 Unit cell: (72.21, 85.26, 71.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 773 8.00 N 665 7.00 C 2397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 865.3 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: 18 helices and 7 sheets defined 58.6% alpha, 10.1% 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: 4.177A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.773A 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 removed outlier: 3.575A pdb=" N GLY K 110 " --> pdb=" O ALA K 106 " (cutoff:3.500A) 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: 3.558A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 359 through 375 removed outlier: 4.053A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.834A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 458 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 5 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: 6.530A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AA5, first strand: chain 'K' and resid 273 through 277 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 removed outlier: 3.670A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 762 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: 1.25 Time building geometry restraints manager: 1.56 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: 490 1.46 - 1.57: 2016 1.57 - 1.69: 0 1.69 - 1.80: 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 1.759 0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" CA MET K 520 " pdb=" CB MET K 520 " ideal model delta sigma weight residual 1.536 1.510 0.026 2.08e-02 2.31e+03 1.54e+00 bond pdb=" CB MET K 520 " pdb=" CG MET K 520 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" CA GLY K 256 " pdb=" C GLY K 256 " ideal model delta sigma weight residual 1.520 1.508 0.012 1.28e-02 6.10e+03 8.15e-01 bond pdb=" SD MET K 16 " pdb=" CE MET K 16 " ideal model delta sigma weight residual 1.791 1.771 0.020 2.50e-02 1.60e+03 6.30e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.01: 69 106.01 - 112.29: 2060 112.29 - 118.58: 1137 118.58 - 124.87: 1962 124.87 - 131.16: 15 Bond angle restraints: 5243 Sorted by residual: angle pdb=" CB MET K 520 " pdb=" CG MET K 520 " pdb=" SD MET K 520 " ideal model delta sigma weight residual 112.70 104.95 7.75 3.00e+00 1.11e-01 6.67e+00 angle pdb=" N ALA K 449 " pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 112.75 115.50 -2.75 1.36e+00 5.41e-01 4.09e+00 angle pdb=" CB MET K 166 " pdb=" CG MET K 166 " pdb=" SD MET K 166 " ideal model delta sigma weight residual 112.70 118.43 -5.73 3.00e+00 1.11e-01 3.64e+00 angle pdb=" C GLU K 409 " pdb=" N GLY K 410 " pdb=" CA GLY K 410 " ideal model delta sigma weight residual 121.45 118.95 2.50 1.54e+00 4.22e-01 2.63e+00 angle pdb=" C ASP K 490 " pdb=" N MET K 491 " pdb=" CA MET K 491 " ideal model delta sigma weight residual 122.65 120.08 2.57 1.60e+00 3.91e-01 2.58e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2262 17.68 - 35.37: 126 35.37 - 53.05: 20 53.05 - 70.73: 3 70.73 - 88.41: 1 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA ASP K 224 " pdb=" CB ASP K 224 " pdb=" CG ASP K 224 " pdb=" OD1 ASP K 224 " ideal model delta sinusoidal sigma weight residual -30.00 -86.40 56.40 1 2.00e+01 2.50e-03 1.07e+01 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 88.41 -88.41 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA MET K 491 " pdb=" C MET K 491 " pdb=" N GLY K 492 " pdb=" CA GLY K 492 " ideal model delta harmonic sigma weight residual 180.00 164.92 15.08 0 5.00e+00 4.00e-02 9.09e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 360 0.024 - 0.048: 159 0.048 - 0.072: 65 0.072 - 0.096: 34 0.096 - 0.120: 20 Chirality restraints: 638 Sorted by residual: 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 3.62e-01 chirality pdb=" CA PRO K 462 " pdb=" N PRO K 462 " pdb=" C PRO K 462 " pdb=" CB PRO K 462 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.62e-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 3.43e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 245 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.45e-01 pdb=" N PRO K 246 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO K 246 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO K 246 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 201 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.33e-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 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 336 " 0.003 2.00e-02 2.50e+03 6.64e-03 4.41e-01 pdb=" C VAL K 336 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL K 336 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY K 337 " 0.004 2.00e-02 2.50e+03 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 247 2.73 - 3.27: 4008 3.27 - 3.82: 6482 3.82 - 4.36: 7028 4.36 - 4.90: 12698 Nonbonded interactions: 30463 Sorted by model distance: nonbonded pdb=" OG1 THR K 299 " pdb=" OD1 ASP K 316 " model vdw 2.190 2.440 nonbonded pdb=" NH2 ARG K 421 " pdb=" O VAL K 469 " model vdw 2.241 2.520 nonbonded pdb=" OD1 ASP K 115 " pdb=" NH2 ARG K 118 " model vdw 2.307 2.520 nonbonded pdb=" O GLY K 35 " pdb=" NZ LYS K 51 " model vdw 2.325 2.520 nonbonded pdb=" OE2 GLU K 214 " pdb=" NH2 ARG K 322 " model vdw 2.336 2.520 ... (remaining 30458 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: 1.180 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: 0.000 Extract box with map and model: 5.700 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 0.032 3883 Z= 0.197 Angle : 0.491 7.745 5243 Z= 0.271 Chirality : 0.039 0.120 638 Planarity : 0.002 0.024 687 Dihedral : 11.427 88.413 1464 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 2.31 (0.36), residues: 522 helix: 2.48 (0.29), residues: 294 sheet: 0.33 (0.51), residues: 88 loop : 0.38 (0.50), residues: 140 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 506 ARG 0.001 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 33 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.387 Fit side-chains REVERT: K 191 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7343 (pt0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2315 time to fit residues: 9.3463 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 0.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3883 Z= 0.235 Angle : 0.505 5.406 5243 Z= 0.271 Chirality : 0.041 0.139 638 Planarity : 0.003 0.027 687 Dihedral : 3.691 15.022 552 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 2.01 (0.35), residues: 522 helix: 2.36 (0.29), residues: 299 sheet: 0.10 (0.56), residues: 72 loop : -0.10 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.010 0.001 PHE K 195 TYR 0.009 0.001 TYR K 199 ARG 0.005 0.000 ARG K 18 *********************** 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 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.434 Fit side-chains REVERT: K 191 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7234 (pt0) REVERT: K 193 MET cc_start: 0.7754 (ptt) cc_final: 0.7121 (ptp) REVERT: K 288 MET cc_start: 0.8580 (mtp) cc_final: 0.8237 (mtm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1589 time to fit residues: 5.6718 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 GLN K 432 GLN ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3883 Z= 0.181 Angle : 0.455 4.982 5243 Z= 0.245 Chirality : 0.039 0.136 638 Planarity : 0.002 0.025 687 Dihedral : 3.644 14.266 552 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 8.17 % Favored : 91.34 % 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 (0.36), residues: 522 helix: 2.34 (0.29), residues: 300 sheet: -0.09 (0.55), residues: 72 loop : -0.05 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.019 0.002 PHE K 44 TYR 0.008 0.001 TYR K 199 ARG 0.003 0.000 ARG K 18 *********************** 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 28 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.486 Fit side-chains REVERT: K 191 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7252 (pt0) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.1236 time to fit residues: 5.0936 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 432 GLN ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3883 Z= 0.188 Angle : 0.472 6.831 5243 Z= 0.250 Chirality : 0.039 0.135 638 Planarity : 0.002 0.024 687 Dihedral : 3.641 14.044 552 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.25 % Allowed : 9.90 % Favored : 89.85 % 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: 2.00 (0.36), residues: 522 helix: 2.36 (0.29), residues: 300 sheet: -0.29 (0.52), residues: 88 loop : 0.18 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.016 0.002 PHE K 44 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** 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 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.385 Fit side-chains REVERT: K 191 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7258 (pt0) REVERT: K 193 MET cc_start: 0.8303 (ppp) cc_final: 0.7178 (ptm) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1266 time to fit residues: 4.8606 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3883 Z= 0.135 Angle : 0.446 5.934 5243 Z= 0.238 Chirality : 0.039 0.139 638 Planarity : 0.002 0.021 687 Dihedral : 3.601 13.648 552 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 10.15 % Favored : 88.86 % 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: 2.12 (0.37), residues: 522 helix: 2.41 (0.29), residues: 302 sheet: -0.29 (0.52), residues: 88 loop : 0.37 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.007 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** 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 29 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.449 Fit side-chains REVERT: K 191 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7164 (pt0) REVERT: K 193 MET cc_start: 0.8414 (ppp) cc_final: 0.8026 (ppp) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.1209 time to fit residues: 5.0326 Evaluate side-chains 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1655 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= 0.140 Angle : 0.426 5.023 5243 Z= 0.231 Chirality : 0.039 0.136 638 Planarity : 0.002 0.021 687 Dihedral : 3.572 14.147 552 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.74 % Allowed : 10.64 % Favored : 88.61 % 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: 2.04 (0.36), residues: 522 helix: 2.46 (0.29), residues: 303 sheet: -0.42 (0.51), residues: 91 loop : 0.09 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.012 0.001 PHE K 44 TYR 0.007 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** 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 29 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.456 Fit side-chains REVERT: K 191 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7176 (pt0) REVERT: K 193 MET cc_start: 0.8465 (ppp) cc_final: 0.8019 (ppp) REVERT: K 506 TYR cc_start: 0.8744 (m-80) cc_final: 0.8486 (m-80) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.1200 time to fit residues: 5.0259 Evaluate side-chains 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3883 Z= 0.134 Angle : 0.445 7.087 5243 Z= 0.235 Chirality : 0.039 0.140 638 Planarity : 0.002 0.022 687 Dihedral : 3.538 13.792 552 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.50 % Allowed : 11.39 % Favored : 88.12 % 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: 2.05 (0.36), residues: 522 helix: 2.46 (0.29), residues: 303 sheet: -0.41 (0.51), residues: 91 loop : 0.12 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.009 0.001 PHE K 195 TYR 0.007 0.001 TYR K 199 ARG 0.002 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.514 Fit side-chains REVERT: K 191 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7179 (pt0) REVERT: K 193 MET cc_start: 0.8485 (ppp) cc_final: 0.8013 (ppp) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1291 time to fit residues: 4.6766 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1696 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= 0.227 Angle : 0.474 8.041 5243 Z= 0.252 Chirality : 0.040 0.132 638 Planarity : 0.002 0.022 687 Dihedral : 3.639 19.761 552 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.50 % Allowed : 11.14 % Favored : 88.37 % 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: 2.06 (0.36), residues: 522 helix: 2.38 (0.29), residues: 303 sheet: -0.24 (0.53), residues: 85 loop : 0.17 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.011 0.001 PHE K 195 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG K 268 *********************** 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 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.419 Fit side-chains REVERT: K 191 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7255 (pt0) REVERT: K 193 MET cc_start: 0.8483 (ppp) cc_final: 0.7984 (ppp) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1206 time to fit residues: 4.3668 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET 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: 0.9980 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3883 Z= 0.142 Angle : 0.471 7.568 5243 Z= 0.250 Chirality : 0.039 0.133 638 Planarity : 0.002 0.023 687 Dihedral : 3.613 17.762 552 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 10.89 % Favored : 88.61 % 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: 2.04 (0.36), residues: 522 helix: 2.37 (0.29), residues: 303 sheet: -0.26 (0.54), residues: 85 loop : 0.18 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.016 0.001 PHE K 44 TYR 0.008 0.001 TYR K 199 ARG 0.002 0.000 ARG K 395 *********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.434 Fit side-chains REVERT: K 191 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7199 (pt0) REVERT: K 193 MET cc_start: 0.8519 (ppp) cc_final: 0.8018 (ppp) REVERT: K 506 TYR cc_start: 0.8738 (m-80) cc_final: 0.8463 (m-80) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1176 time to fit residues: 4.2496 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3883 Z= 0.177 Angle : 0.511 11.269 5243 Z= 0.264 Chirality : 0.040 0.142 638 Planarity : 0.002 0.022 687 Dihedral : 3.689 14.023 552 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 10.89 % Favored : 88.61 % 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: 1.92 (0.36), residues: 522 helix: 2.26 (0.29), residues: 303 sheet: -0.28 (0.54), residues: 85 loop : 0.14 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.014 0.001 PHE K 44 TYR 0.008 0.001 TYR K 199 ARG 0.001 0.000 ARG K 395 ********************** 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 26 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.483 Fit side-chains REVERT: K 191 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7207 (pt0) REVERT: K 193 MET cc_start: 0.8507 (ppp) cc_final: 0.7974 (ppp) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.1243 time to fit residues: 4.5204 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 453 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 = 0.3409 r_free = 0.3409 target = 0.076679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063405 restraints weight = 11055.513| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.88 r_work: 0.2972 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3883 Z= 0.296 Angle : 0.591 16.627 5243 Z= 0.297 Chirality : 0.041 0.135 638 Planarity : 0.002 0.024 687 Dihedral : 3.793 15.840 552 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.25 % Allowed : 10.89 % Favored : 88.86 % 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: 1.87 (0.36), residues: 522 helix: 2.26 (0.29), residues: 302 sheet: -0.34 (0.53), residues: 85 loop : 0.06 (0.52), residues: 135 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 0.010 0.001 TYR K 199 ARG 0.004 0.000 ARG K 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1036.96 seconds wall clock time: 19 minutes 31.12 seconds (1171.12 seconds total)