Starting phenix.real_space_refine on Thu Dec 7 20:01:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/12_2023/7sk2_25170_updated.pdb" } resolution = 3.82 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= 0.019 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 35 5.16 5 C 2788 2.51 5 N 651 2.21 5 O 703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4177 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4177 Unusual residues: {'TGI': 1} Classifications: {'peptide': 532, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 509, None: 1} Not linked: pdbres="VAL A 578 " pdbres="TGI A 601 " Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.76, per 1000 atoms: 0.66 Number of scatterers: 4177 At special positions: 0 Unit cell: (83.739, 73.17, 77.235, 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 35 16.00 O 703 8.00 N 651 7.00 C 2788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " 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: 2.14 Conformation dependent library (CDL) restraints added in 761.3 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 66.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.559A pdb=" N MET A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 81 through 84 No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.962A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.758A pdb=" N CYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 246 through 258 removed outlier: 3.791A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 316 through 348 removed outlier: 4.203A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 361 through 373 removed outlier: 4.624A pdb=" N ALA A 364 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 367 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR A 368 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.524A pdb=" N VAL A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 3.919A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 432 through 439 removed outlier: 6.303A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 477 through 488 removed outlier: 4.423A pdb=" N ASP A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.559A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'A' and resid 563 through 568 removed outlier: 4.134A pdb=" N ILE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 528 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: 1.14 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1211 1.34 - 1.46: 1142 1.46 - 1.58: 1904 1.58 - 1.70: 4 1.70 - 1.82: 52 Bond restraints: 4313 Sorted by residual: bond pdb=" C21 TGI A 601 " pdb=" C22 TGI A 601 " ideal model delta sigma weight residual 1.599 1.430 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C02 TGI A 601 " pdb=" C06 TGI A 601 " ideal model delta sigma weight residual 1.599 1.433 0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C03 TGI A 601 " pdb=" S04 TGI A 601 " ideal model delta sigma weight residual 1.558 1.690 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C20 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.558 1.687 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C23 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.560 1.688 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 4308 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.34: 101 105.34 - 112.56: 2047 112.56 - 119.78: 1558 119.78 - 127.01: 2098 127.01 - 134.23: 79 Bond angle restraints: 5883 Sorted by residual: angle pdb=" C07 TGI A 601 " pdb=" C08 TGI A 601 " pdb=" C09 TGI A 601 " ideal model delta sigma weight residual 85.79 122.57 -36.78 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C03 TGI A 601 " pdb=" C07 TGI A 601 " pdb=" C20 TGI A 601 " ideal model delta sigma weight residual 92.38 118.60 -26.22 3.00e+00 1.11e-01 7.64e+01 angle pdb=" C ILE A 377 " pdb=" N SER A 378 " pdb=" CA SER A 378 " ideal model delta sigma weight residual 120.58 127.09 -6.51 1.32e+00 5.74e-01 2.43e+01 angle pdb=" CB LYS A 350 " pdb=" CG LYS A 350 " pdb=" CD LYS A 350 " ideal model delta sigma weight residual 111.30 122.26 -10.96 2.30e+00 1.89e-01 2.27e+01 angle pdb=" CA VAL A 58 " pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 110.40 117.16 -6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 5878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2197 16.93 - 33.86: 176 33.86 - 50.80: 38 50.80 - 67.73: 7 67.73 - 84.66: 4 Dihedral angle restraints: 2422 sinusoidal: 892 harmonic: 1530 Sorted by residual: dihedral pdb=" CA PHE A 480 " pdb=" C PHE A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 380 0.039 - 0.079: 170 0.079 - 0.118: 59 0.118 - 0.157: 24 0.157 - 0.197: 9 Chirality restraints: 642 Sorted by residual: chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE A 341 " pdb=" CA ILE A 341 " pdb=" CG1 ILE A 341 " pdb=" CG2 ILE A 341 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA SER A 378 " pdb=" N SER A 378 " pdb=" C SER A 378 " pdb=" CB SER A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 639 not shown) Planarity restraints: 722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASN A 137 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN A 137 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 138 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 136 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN A 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 138 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.09e+00 pdb=" C ILE A 138 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 138 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 139 " 0.017 2.00e-02 2.50e+03 ... (remaining 719 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 830 2.77 - 3.30: 4270 3.30 - 3.83: 7364 3.83 - 4.37: 8397 4.37 - 4.90: 13735 Nonbonded interactions: 34596 Sorted by model distance: nonbonded pdb=" OH TYR A 296 " pdb=" OG SER A 328 " model vdw 2.235 2.440 nonbonded pdb=" O VAL A 142 " pdb=" OG SER A 145 " model vdw 2.250 2.440 nonbonded pdb=" O PHE A 92 " pdb=" OG1 THR A 504 " model vdw 2.264 2.440 nonbonded pdb=" O PHE A 450 " pdb=" OG SER A 454 " model vdw 2.265 2.440 nonbonded pdb=" O SER A 437 " pdb=" OG1 THR A 440 " model vdw 2.285 2.440 ... (remaining 34591 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 group one per residue 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: 0.790 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: 3.630 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.780 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 0.169 4313 Z= 0.505 Angle : 1.216 36.780 5883 Z= 0.580 Chirality : 0.055 0.197 642 Planarity : 0.006 0.044 722 Dihedral : 13.672 84.661 1447 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -2.59 (0.34), residues: 530 helix: -1.32 (0.26), residues: 346 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.037 0.003 PHE A 480 TYR 0.039 0.003 TYR A 452 ARG 0.005 0.001 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1451 time to fit residues: 25.4215 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4313 Z= 0.214 Angle : 0.759 17.278 5883 Z= 0.365 Chirality : 0.042 0.136 642 Planarity : 0.005 0.032 722 Dihedral : 7.124 65.024 585 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.82 % Allowed : 12.68 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.36), residues: 530 helix: -0.74 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.92 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 230 HIS 0.009 0.002 HIS A 347 PHE 0.017 0.002 PHE A 122 TYR 0.024 0.002 TYR A 551 ARG 0.004 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 127 average time/residue: 0.1350 time to fit residues: 22.4229 Evaluate side-chains 127 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0489 time to fit residues: 1.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4313 Z= 0.229 Angle : 0.751 18.154 5883 Z= 0.358 Chirality : 0.042 0.162 642 Planarity : 0.004 0.029 722 Dihedral : 7.007 66.447 585 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.41 % Allowed : 18.54 % Favored : 80.05 % 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 (0.37), residues: 530 helix: -0.46 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 168 HIS 0.008 0.003 HIS A 347 PHE 0.023 0.002 PHE A 385 TYR 0.021 0.002 TYR A 139 ARG 0.005 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 0.482 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.1324 time to fit residues: 21.0644 Evaluate side-chains 117 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0453 time to fit residues: 0.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4313 Z= 0.175 Angle : 0.717 18.090 5883 Z= 0.340 Chirality : 0.041 0.144 642 Planarity : 0.004 0.026 722 Dihedral : 6.895 66.877 585 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.41 % Allowed : 20.66 % Favored : 77.93 % 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: -0.99 (0.38), residues: 530 helix: -0.19 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.45 (0.52), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 135 HIS 0.008 0.002 HIS A 347 PHE 0.018 0.002 PHE A 385 TYR 0.019 0.001 TYR A 139 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.446 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 120 average time/residue: 0.1409 time to fit residues: 21.9198 Evaluate side-chains 116 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0513 time to fit residues: 1.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN A 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4313 Z= 0.210 Angle : 0.740 18.007 5883 Z= 0.352 Chirality : 0.041 0.166 642 Planarity : 0.004 0.026 722 Dihedral : 6.857 68.117 585 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.88 % Allowed : 23.47 % Favored : 74.65 % 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: -0.92 (0.38), residues: 530 helix: -0.12 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.46 (0.51), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 135 HIS 0.008 0.002 HIS A 347 PHE 0.018 0.002 PHE A 385 TYR 0.020 0.002 TYR A 139 ARG 0.001 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.500 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1265 time to fit residues: 20.5684 Evaluate side-chains 118 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0385 time to fit residues: 0.9344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4313 Z= 0.188 Angle : 0.743 17.975 5883 Z= 0.352 Chirality : 0.041 0.158 642 Planarity : 0.004 0.026 722 Dihedral : 6.828 68.749 585 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 25.12 % Favored : 73.00 % 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: -0.75 (0.38), residues: 530 helix: 0.03 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.41 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 135 HIS 0.008 0.002 HIS A 347 PHE 0.017 0.002 PHE A 385 TYR 0.019 0.002 TYR A 139 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.474 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1313 time to fit residues: 21.0715 Evaluate side-chains 121 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0420 time to fit residues: 1.0688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4313 Z= 0.203 Angle : 0.753 17.960 5883 Z= 0.359 Chirality : 0.041 0.148 642 Planarity : 0.004 0.026 722 Dihedral : 6.855 69.567 585 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.41 % Allowed : 26.06 % Favored : 72.54 % 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: -0.70 (0.38), residues: 530 helix: 0.04 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.34 (0.51), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 135 HIS 0.009 0.003 HIS A 347 PHE 0.018 0.002 PHE A 386 TYR 0.019 0.001 TYR A 139 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 0.499 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.1352 time to fit residues: 21.6212 Evaluate side-chains 120 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0454 time to fit residues: 0.9589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 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 153 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4313 Z= 0.184 Angle : 0.764 18.004 5883 Z= 0.360 Chirality : 0.042 0.156 642 Planarity : 0.004 0.025 722 Dihedral : 6.876 69.302 585 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.17 % Allowed : 27.93 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.38), residues: 530 helix: 0.12 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 135 HIS 0.009 0.003 HIS A 347 PHE 0.017 0.002 PHE A 293 TYR 0.018 0.001 TYR A 139 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 0.477 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 123 average time/residue: 0.1363 time to fit residues: 21.8859 Evaluate side-chains 122 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0501 time to fit residues: 0.9711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4313 Z= 0.185 Angle : 0.777 18.046 5883 Z= 0.367 Chirality : 0.042 0.181 642 Planarity : 0.004 0.025 722 Dihedral : 6.848 69.103 585 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.94 % Allowed : 27.93 % Favored : 71.13 % 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: -0.56 (0.38), residues: 530 helix: 0.17 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.30 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 135 HIS 0.010 0.003 HIS A 347 PHE 0.036 0.002 PHE A 404 TYR 0.030 0.002 TYR A 551 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.480 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 119 average time/residue: 0.1428 time to fit residues: 22.7205 Evaluate side-chains 118 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0648 time to fit residues: 0.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4313 Z= 0.186 Angle : 0.792 18.096 5883 Z= 0.375 Chirality : 0.042 0.190 642 Planarity : 0.004 0.025 722 Dihedral : 6.820 68.812 585 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.23 % Allowed : 28.87 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.38), residues: 530 helix: 0.11 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.36 (0.51), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 135 HIS 0.008 0.002 HIS A 347 PHE 0.017 0.002 PHE A 386 TYR 0.019 0.001 TYR A 139 ARG 0.001 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.467 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 115 average time/residue: 0.1288 time to fit residues: 19.7335 Evaluate side-chains 116 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0470 time to fit residues: 0.7519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 163 GLN A 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.162777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140189 restraints weight = 9280.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143800 restraints weight = 5737.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146530 restraints weight = 4054.285| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4313 Z= 0.174 Angle : 0.783 18.109 5883 Z= 0.368 Chirality : 0.042 0.181 642 Planarity : 0.004 0.026 722 Dihedral : 6.756 68.235 585 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.70 % Allowed : 28.87 % Favored : 70.42 % 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: -0.41 (0.38), residues: 530 helix: 0.23 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.15 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 135 HIS 0.008 0.002 HIS A 347 PHE 0.040 0.002 PHE A 404 TYR 0.019 0.001 TYR A 139 ARG 0.002 0.000 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.92 seconds wall clock time: 28 minutes 47.67 seconds (1727.67 seconds total)