Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 21:50:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/10_2023/7xop_33355.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/10_2023/7xop_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_33355/10_2023/7xop_33355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/10_2023/7xop_33355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/10_2023/7xop_33355.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xop_33355/10_2023/7xop_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-1.21rc1-5097/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: 2.61, per 1000 atoms: 0.68 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: 1.57 Conformation dependent library (CDL) restraints added in 746.6 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: 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: 0.39 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: 1.08 Time building geometry restraints manager: 1.71 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: 1.140 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: 5.640 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.110 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2437 time to fit residues: 9.8587 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5378 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1001 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= 0.236 Angle : 0.501 5.259 5243 Z= 0.270 Chirality : 0.041 0.142 638 Planarity : 0.003 0.026 687 Dihedral : 3.691 14.773 552 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: 2.03 (0.35), residues: 522 helix: 2.38 (0.29), residues: 299 sheet: 0.12 (0.55), residues: 72 loop : -0.09 (0.47), residues: 151 *********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1697 time to fit residues: 5.8590 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6297 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 24 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 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: 0.8430 moved from start: 0.1280 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= 0.211 Angle : 0.470 4.986 5243 Z= 0.252 Chirality : 0.040 0.136 638 Planarity : 0.002 0.025 687 Dihedral : 3.676 14.587 552 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.50 % Allowed : 8.66 % Favored : 90.84 % 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: 1.95 (0.36), residues: 522 helix: 2.31 (0.29), residues: 299 sheet: -0.18 (0.51), residues: 88 loop : 0.09 (0.52), residues: 135 *********************** 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 27 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.477 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.1260 time to fit residues: 5.0152 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6215 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.1453 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= 0.190 Angle : 0.471 5.848 5243 Z= 0.250 Chirality : 0.039 0.135 638 Planarity : 0.002 0.024 687 Dihedral : 3.668 14.235 552 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.25 % Allowed : 10.40 % Favored : 89.36 % 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: 1.96 (0.36), residues: 522 helix: 2.30 (0.29), residues: 300 sheet: -0.20 (0.51), residues: 88 loop : 0.16 (0.52), residues: 134 *********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.476 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1231 time to fit residues: 4.6497 Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6216 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3883 Z= 0.198 Angle : 0.464 6.186 5243 Z= 0.248 Chirality : 0.039 0.135 638 Planarity : 0.002 0.022 687 Dihedral : 3.652 14.120 552 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 10.89 % 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: 2.00 (0.36), residues: 522 helix: 2.36 (0.29), residues: 300 sheet: -0.27 (0.51), residues: 88 loop : 0.17 (0.52), residues: 134 *********************** 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 28 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.477 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.1187 time to fit residues: 4.8510 Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0621 time to fit residues: 0.7255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3883 Z= 0.255 Angle : 0.489 6.529 5243 Z= 0.260 Chirality : 0.040 0.132 638 Planarity : 0.002 0.022 687 Dihedral : 3.707 15.110 552 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 11.63 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.36), residues: 522 helix: 2.36 (0.29), residues: 299 sheet: -0.32 (0.52), residues: 85 loop : 0.00 (0.50), residues: 138 *********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.474 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.1257 time to fit residues: 4.5750 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.8164 ------------------------------------------------------------------------------- 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: 0.8447 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3883 Z= 0.238 Angle : 0.481 6.920 5243 Z= 0.258 Chirality : 0.040 0.133 638 Planarity : 0.002 0.022 687 Dihedral : 3.737 17.335 552 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.36), residues: 522 helix: 2.27 (0.29), residues: 302 sheet: -0.34 (0.52), residues: 85 loop : -0.08 (0.50), residues: 135 *********************** 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 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1212 time to fit residues: 4.0796 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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: 0.8437 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3883 Z= 0.205 Angle : 0.473 7.274 5243 Z= 0.253 Chirality : 0.039 0.133 638 Planarity : 0.002 0.022 687 Dihedral : 3.664 14.208 552 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.25 % Allowed : 13.12 % Favored : 86.63 % 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: 1.90 (0.36), residues: 522 helix: 2.33 (0.29), residues: 302 sheet: -0.35 (0.52), residues: 85 loop : -0.03 (0.51), residues: 135 *********************** 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 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.487 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1284 time to fit residues: 4.4788 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.1866 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= 0.233 Angle : 0.481 6.887 5243 Z= 0.258 Chirality : 0.040 0.133 638 Planarity : 0.002 0.022 687 Dihedral : 3.675 14.315 552 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.25 % Allowed : 12.87 % Favored : 86.88 % 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: 1.85 (0.36), residues: 522 helix: 2.30 (0.29), residues: 302 sheet: -0.37 (0.52), residues: 85 loop : -0.09 (0.51), residues: 135 *********************** 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 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.483 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.1264 time to fit residues: 4.4063 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8417 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3883 Z= 0.167 Angle : 0.479 7.836 5243 Z= 0.255 Chirality : 0.039 0.138 638 Planarity : 0.002 0.022 687 Dihedral : 3.611 14.093 552 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.25 % Allowed : 13.37 % 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: 1.93 (0.36), residues: 522 helix: 2.29 (0.29), residues: 303 sheet: -0.31 (0.52), residues: 85 loop : 0.10 (0.53), residues: 134 ********************** 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 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.457 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1228 time to fit residues: 4.6138 Evaluate side-chains 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 overall best weight: 2.3482 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.076531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063243 restraints weight = 11029.789| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.90 r_work: 0.2980 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1971 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= 0.218 Angle : 0.503 9.969 5243 Z= 0.268 Chirality : 0.040 0.135 638 Planarity : 0.002 0.022 687 Dihedral : 3.643 14.064 552 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.25 % Allowed : 13.61 % Favored : 86.14 % 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: 2.25 (0.29), residues: 303 sheet: -0.31 (0.53), residues: 85 loop : 0.06 (0.52), residues: 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1007.80 seconds wall clock time: 18 minutes 57.14 seconds (1137.14 seconds total)