Starting phenix.real_space_refine on Sun Mar 10 18:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/03_2024/7wn1_32619_updated.pdb" } resolution = 3.11 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= 0.033 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 26 5.16 5 C 2572 2.51 5 N 616 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.76, per 1000 atoms: 0.71 Number of scatterers: 3901 At special positions: 0 Unit cell: (110.39, 60.59, 64.74, 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 26 16.00 O 687 8.00 N 616 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 58.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 32 through 58 removed outlier: 4.331A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 82 removed outlier: 4.022A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 110 removed outlier: 3.848A pdb=" N LEU A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.700A pdb=" N PHE A 110 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 143 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.802A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 209 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.625A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 3.759A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 310 through 331 removed outlier: 3.597A pdb=" N LEU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.661A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 368 removed outlier: 3.804A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.181A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 404 removed outlier: 3.684A pdb=" N THR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing sheet with id= A, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.513A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 100 removed outlier: 3.585A pdb=" N GLN C 109 " --> pdb=" O THR C 99 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 823 1.33 - 1.45: 929 1.45 - 1.57: 2205 1.57 - 1.69: 2 1.69 - 1.81: 39 Bond restraints: 3998 Sorted by residual: bond pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.50e-02 4.44e+03 1.53e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.526 1.346 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.454 1.309 0.145 1.50e-02 4.44e+03 9.32e+01 bond pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.293 1.444 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C4 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.347 1.497 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 87 107.08 - 113.80: 2264 113.80 - 120.52: 1589 120.52 - 127.25: 1448 127.25 - 133.97: 41 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 114.60 107.68 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" C5' NOS A 501 " ideal model delta sigma weight residual 115.20 109.44 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C4' NOS A 501 " ideal model delta sigma weight residual 109.70 106.15 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C2' NOS A 501 " pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 114.00 108.75 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sigma weight residual 101.50 104.96 -3.46 1.00e+00 1.00e+00 1.20e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2049 15.24 - 30.48: 201 30.48 - 45.71: 53 45.71 - 60.95: 17 60.95 - 76.19: 3 Dihedral angle restraints: 2323 sinusoidal: 899 harmonic: 1424 Sorted by residual: dihedral pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sinusoidal sigma weight residual 24.00 -2.88 26.88 1 8.00e+00 1.56e-02 1.62e+01 dihedral pdb=" C1' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sinusoidal sigma weight residual 2.00 -22.80 24.80 1 8.00e+00 1.56e-02 1.38e+01 dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 173 0.061 - 0.092: 57 0.092 - 0.122: 20 0.122 - 0.153: 8 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ASP A 147 " pdb=" N ASP A 147 " pdb=" C ASP A 147 " pdb=" CB ASP A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE A 307 " pdb=" N PHE A 307 " pdb=" C PHE A 307 " pdb=" CB PHE A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 627 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 334 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 335 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 413 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.017 5.00e-02 4.00e+02 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 835 2.78 - 3.31: 3868 3.31 - 3.84: 6578 3.84 - 4.37: 7928 4.37 - 4.90: 13692 Nonbonded interactions: 32901 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.246 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 209 " model vdw 2.256 2.440 nonbonded pdb=" O CYS A 395 " pdb=" OG1 THR A 399 " model vdw 2.283 2.440 nonbonded pdb=" O LEU A 256 " pdb=" N GLY A 261 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN C 81 " pdb=" OD1 ASN C 83 " model vdw 2.320 2.520 ... (remaining 32896 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.840 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.710 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 3998 Z= 0.468 Angle : 0.648 10.003 5429 Z= 0.352 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.827 76.187 1406 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.38), residues: 487 helix: 1.09 (0.30), residues: 285 sheet: 0.84 (0.64), residues: 58 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.016 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.446 Fit side-chains REVERT: A 175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m) REVERT: A 303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt) REVERT: A 407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0) REVERT: C 94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1531 time to fit residues: 14.1863 Evaluate side-chains 62 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3998 Z= 0.192 Angle : 0.549 6.561 5429 Z= 0.296 Chirality : 0.042 0.133 630 Planarity : 0.005 0.033 665 Dihedral : 5.585 38.400 540 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.09 % Allowed : 5.58 % Favored : 92.33 % 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: 1.32 (0.38), residues: 487 helix: 1.43 (0.29), residues: 280 sheet: 0.98 (0.64), residues: 58 loop : -0.11 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.003 0.001 HIS A 180 PHE 0.017 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.002 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.438 Fit side-chains REVERT: A 175 VAL cc_start: 0.8093 (t) cc_final: 0.7835 (m) REVERT: A 303 LYS cc_start: 0.8640 (tppt) cc_final: 0.8429 (tppt) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.1462 time to fit residues: 12.5802 Evaluate side-chains 64 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3998 Z= 0.210 Angle : 0.526 6.399 5429 Z= 0.285 Chirality : 0.042 0.131 630 Planarity : 0.004 0.038 665 Dihedral : 5.216 32.630 540 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 10.23 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.38), residues: 487 helix: 1.53 (0.29), residues: 278 sheet: 1.10 (0.64), residues: 58 loop : -0.07 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.016 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.452 Fit side-chains REVERT: A 175 VAL cc_start: 0.8100 (t) cc_final: 0.7853 (m) REVERT: A 303 LYS cc_start: 0.8653 (tppt) cc_final: 0.8434 (tppt) REVERT: C 19 ARG cc_start: 0.8518 (mtp85) cc_final: 0.8142 (mtp-110) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.1662 time to fit residues: 13.0540 Evaluate side-chains 66 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.0050 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 54 ASN A 284 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3998 Z= 0.322 Angle : 0.582 6.156 5429 Z= 0.316 Chirality : 0.044 0.138 630 Planarity : 0.004 0.036 665 Dihedral : 5.279 30.956 540 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 12.33 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.37), residues: 487 helix: 1.24 (0.29), residues: 286 sheet: 0.91 (0.63), residues: 59 loop : -0.18 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 251 HIS 0.003 0.001 HIS A 180 PHE 0.016 0.001 PHE C 27 TYR 0.019 0.002 TYR C 102 ARG 0.003 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.500 Fit side-chains REVERT: A 113 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: C 19 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8160 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.1585 time to fit residues: 13.9628 Evaluate side-chains 69 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.208 Angle : 0.525 6.368 5429 Z= 0.283 Chirality : 0.042 0.262 630 Planarity : 0.004 0.038 665 Dihedral : 5.039 28.228 540 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.79 % Allowed : 13.26 % Favored : 83.95 % 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: 1.40 (0.38), residues: 487 helix: 1.43 (0.30), residues: 285 sheet: 0.98 (0.64), residues: 58 loop : 0.05 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.014 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.411 Fit side-chains REVERT: C 19 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8141 (mtp-110) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1563 time to fit residues: 12.7266 Evaluate side-chains 70 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3998 Z= 0.162 Angle : 0.512 8.211 5429 Z= 0.269 Chirality : 0.041 0.232 630 Planarity : 0.004 0.042 665 Dihedral : 4.783 26.708 540 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 13.26 % Favored : 83.72 % 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: 1.65 (0.38), residues: 487 helix: 1.70 (0.30), residues: 277 sheet: 1.01 (0.65), residues: 58 loop : 0.10 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.465 Fit side-chains REVERT: A 113 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: C 19 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8107 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.1485 time to fit residues: 13.1356 Evaluate side-chains 70 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3998 Z= 0.153 Angle : 0.502 7.229 5429 Z= 0.264 Chirality : 0.040 0.196 630 Planarity : 0.004 0.042 665 Dihedral : 4.651 28.133 540 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.56 % Allowed : 14.65 % Favored : 82.79 % 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: 1.86 (0.39), residues: 487 helix: 1.87 (0.30), residues: 277 sheet: 1.26 (0.66), residues: 58 loop : 0.13 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.520 Fit side-chains REVERT: A 113 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (m-30) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.1389 time to fit residues: 12.0800 Evaluate side-chains 69 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3998 Z= 0.166 Angle : 0.506 7.352 5429 Z= 0.267 Chirality : 0.040 0.185 630 Planarity : 0.004 0.043 665 Dihedral : 4.604 28.621 540 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.79 % Allowed : 15.58 % Favored : 81.63 % 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: 1.88 (0.39), residues: 487 helix: 1.86 (0.30), residues: 278 sheet: 1.35 (0.67), residues: 58 loop : 0.15 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.427 Fit side-chains REVERT: A 113 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: A 175 VAL cc_start: 0.7995 (t) cc_final: 0.7787 (m) outliers start: 12 outliers final: 11 residues processed: 65 average time/residue: 0.1355 time to fit residues: 11.5836 Evaluate side-chains 70 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3998 Z= 0.199 Angle : 0.518 7.238 5429 Z= 0.274 Chirality : 0.041 0.180 630 Planarity : 0.004 0.042 665 Dihedral : 4.657 28.168 540 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 15.35 % Favored : 81.63 % 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: 1.80 (0.38), residues: 487 helix: 1.80 (0.30), residues: 278 sheet: 1.33 (0.66), residues: 58 loop : 0.11 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.012 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.425 Fit side-chains REVERT: A 113 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7903 (m-30) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.1342 time to fit residues: 11.6361 Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3998 Z= 0.171 Angle : 0.507 7.155 5429 Z= 0.268 Chirality : 0.041 0.178 630 Planarity : 0.004 0.042 665 Dihedral : 4.588 28.101 540 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 15.35 % Favored : 81.63 % 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: 1.91 (0.39), residues: 487 helix: 1.87 (0.30), residues: 278 sheet: 1.39 (0.66), residues: 58 loop : 0.17 (0.56), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.501 Fit side-chains REVERT: A 113 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: A 175 VAL cc_start: 0.8023 (t) cc_final: 0.7816 (m) outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.1416 time to fit residues: 11.8906 Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099601 restraints weight = 5103.474| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.62 r_work: 0.3053 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3998 Z= 0.202 Angle : 0.519 7.062 5429 Z= 0.275 Chirality : 0.041 0.176 630 Planarity : 0.004 0.042 665 Dihedral : 4.650 28.095 540 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 15.35 % Favored : 81.63 % 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: 1.84 (0.38), residues: 487 helix: 1.80 (0.30), residues: 278 sheet: 1.39 (0.66), residues: 58 loop : 0.15 (0.57), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.012 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1299.88 seconds wall clock time: 24 minutes 12.60 seconds (1452.60 seconds total)