Starting phenix.real_space_refine on Sun Mar 10 19:01:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_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_25170/03_2024/7sk2_25170_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_25170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/03_2024/7sk2_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-dev-5265/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: 2.80, per 1000 atoms: 0.67 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: 1.71 Conformation dependent library (CDL) restraints added in 672.2 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: 0.89 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: 0.98 Time building geometry restraints manager: 1.86 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: 0.690 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: 3.580 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.510 Find NCS groups from input model: 0.140 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- 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 : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7822 (tmm) cc_final: 0.7527 (tmm) REVERT: A 283 GLU cc_start: 0.8133 (pp20) cc_final: 0.7926 (pp20) REVERT: A 292 ILE cc_start: 0.8583 (mm) cc_final: 0.8317 (mm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1407 time to fit residues: 24.3130 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.198 Angle : 0.751 17.264 5883 Z= 0.359 Chirality : 0.041 0.127 642 Planarity : 0.004 0.032 722 Dihedral : 7.108 65.147 585 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.58 % Allowed : 12.68 % Favored : 84.74 % 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: -1.73 (0.36), residues: 530 helix: -0.68 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.93 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 230 HIS 0.009 0.002 HIS A 347 PHE 0.017 0.002 PHE A 122 TYR 0.023 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 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8592 (tttm) cc_final: 0.7803 (tptp) REVERT: A 77 ASN cc_start: 0.8286 (m-40) cc_final: 0.7484 (m110) REVERT: A 200 MET cc_start: 0.6731 (tpt) cc_final: 0.6357 (mmm) REVERT: A 269 LEU cc_start: 0.7642 (mm) cc_final: 0.7427 (mm) REVERT: A 283 GLU cc_start: 0.8256 (pp20) cc_final: 0.7463 (pp20) REVERT: A 287 ASP cc_start: 0.7953 (m-30) cc_final: 0.7557 (m-30) REVERT: A 321 ILE cc_start: 0.8283 (pt) cc_final: 0.8075 (pt) outliers start: 11 outliers final: 10 residues processed: 127 average time/residue: 0.1377 time to fit residues: 22.8212 Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP 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: 2.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7056 moved from start: 0.2138 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= 0.169 Angle : 0.732 18.175 5883 Z= 0.343 Chirality : 0.040 0.159 642 Planarity : 0.004 0.029 722 Dihedral : 6.869 65.454 585 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.05 % Allowed : 18.31 % Favored : 78.64 % 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: -1.22 (0.37), residues: 530 helix: -0.30 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.71 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.008 0.002 HIS A 347 PHE 0.027 0.002 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.004 0.000 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 133 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8279 (m-40) cc_final: 0.7844 (m-40) REVERT: A 200 MET cc_start: 0.6754 (tpt) cc_final: 0.6349 (mmm) REVERT: A 269 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7429 (mm) REVERT: A 283 GLU cc_start: 0.8253 (pp20) cc_final: 0.7559 (pp20) REVERT: A 287 ASP cc_start: 0.7961 (m-30) cc_final: 0.7348 (m-30) REVERT: A 321 ILE cc_start: 0.8340 (pt) cc_final: 0.8075 (pt) REVERT: A 462 PHE cc_start: 0.8625 (t80) cc_final: 0.8415 (t80) REVERT: A 479 ARG cc_start: 0.7563 (ptt180) cc_final: 0.7319 (ptt180) REVERT: A 545 MET cc_start: 0.8423 (mmt) cc_final: 0.8187 (mmt) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.1299 time to fit residues: 21.0570 Evaluate side-chains 126 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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: 0.7031 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4313 Z= 0.159 Angle : 0.708 18.156 5883 Z= 0.330 Chirality : 0.040 0.155 642 Planarity : 0.004 0.028 722 Dihedral : 6.747 65.671 585 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 20.19 % Favored : 77.00 % 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: -0.94 (0.37), residues: 530 helix: -0.07 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.62 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 135 HIS 0.009 0.002 HIS A 347 PHE 0.020 0.002 PHE A 385 TYR 0.018 0.001 TYR A 139 ARG 0.004 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 133 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8344 (m-40) cc_final: 0.7887 (m-40) REVERT: A 168 TRP cc_start: 0.5954 (p90) cc_final: 0.5686 (p90) REVERT: A 198 HIS cc_start: 0.7182 (m90) cc_final: 0.6900 (m-70) REVERT: A 200 MET cc_start: 0.6691 (tpt) cc_final: 0.6314 (mmm) REVERT: A 269 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7451 (mm) REVERT: A 283 GLU cc_start: 0.8257 (pp20) cc_final: 0.7540 (pp20) REVERT: A 287 ASP cc_start: 0.7942 (m-30) cc_final: 0.7246 (m-30) REVERT: A 321 ILE cc_start: 0.8294 (pt) cc_final: 0.8022 (pt) REVERT: A 462 PHE cc_start: 0.8559 (t80) cc_final: 0.8331 (t80) REVERT: A 479 ARG cc_start: 0.7470 (ptt180) cc_final: 0.7221 (ptt180) REVERT: A 545 MET cc_start: 0.8336 (mmt) cc_final: 0.8038 (mmt) outliers start: 12 outliers final: 11 residues processed: 122 average time/residue: 0.1408 time to fit residues: 22.3490 Evaluate side-chains 128 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP 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: 2.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4313 Z= 0.267 Angle : 0.762 17.920 5883 Z= 0.367 Chirality : 0.042 0.146 642 Planarity : 0.004 0.031 722 Dihedral : 6.861 68.326 585 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.23 % Allowed : 20.66 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.37), residues: 530 helix: -0.19 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.62 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 135 HIS 0.009 0.003 HIS A 347 PHE 0.027 0.002 PHE A 404 TYR 0.023 0.002 TYR A 152 ARG 0.003 0.001 ARG A 566 *********************** 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 139 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.457 Fit side-chains REVERT: A 77 ASN cc_start: 0.8515 (m-40) cc_final: 0.8014 (m110) REVERT: A 168 TRP cc_start: 0.6284 (p90) cc_final: 0.6065 (p90) REVERT: A 174 PHE cc_start: 0.6606 (p90) cc_final: 0.5738 (p90) REVERT: A 200 MET cc_start: 0.6928 (tpt) cc_final: 0.6610 (mmm) REVERT: A 269 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 283 GLU cc_start: 0.8443 (pp20) cc_final: 0.7711 (pp20) REVERT: A 287 ASP cc_start: 0.8108 (m-30) cc_final: 0.7324 (m-30) REVERT: A 321 ILE cc_start: 0.8304 (pt) cc_final: 0.7950 (pt) REVERT: A 545 MET cc_start: 0.8480 (mmt) cc_final: 0.8254 (mmt) outliers start: 18 outliers final: 15 residues processed: 127 average time/residue: 0.1413 time to fit residues: 23.2550 Evaluate side-chains 131 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2916 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= 0.188 Angle : 0.726 17.319 5883 Z= 0.345 Chirality : 0.041 0.152 642 Planarity : 0.004 0.026 722 Dihedral : 6.771 69.362 585 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.69 % Allowed : 21.13 % Favored : 74.18 % 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: -0.69 (0.38), residues: 530 helix: 0.09 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.36 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 135 HIS 0.009 0.002 HIS A 347 PHE 0.017 0.001 PHE A 404 TYR 0.017 0.001 TYR A 139 ARG 0.002 0.000 ARG A 566 *********************** 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 141 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8431 (m-40) cc_final: 0.8031 (m-40) REVERT: A 198 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.7035 (m90) REVERT: A 200 MET cc_start: 0.6892 (tpt) cc_final: 0.6322 (mmm) REVERT: A 269 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 283 GLU cc_start: 0.8404 (pp20) cc_final: 0.7737 (pp20) REVERT: A 287 ASP cc_start: 0.8014 (m-30) cc_final: 0.7333 (m-30) REVERT: A 321 ILE cc_start: 0.8257 (pt) cc_final: 0.7935 (pt) REVERT: A 386 PHE cc_start: 0.8535 (m-80) cc_final: 0.8289 (m-80) REVERT: A 487 MET cc_start: 0.7164 (tpp) cc_final: 0.6137 (tpp) REVERT: A 545 MET cc_start: 0.8474 (mmt) cc_final: 0.8252 (mmt) outliers start: 20 outliers final: 15 residues processed: 127 average time/residue: 0.1276 time to fit residues: 21.2964 Evaluate side-chains 133 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7085 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.177 Angle : 0.741 17.873 5883 Z= 0.348 Chirality : 0.041 0.146 642 Planarity : 0.004 0.026 722 Dihedral : 6.703 68.837 585 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.99 % Allowed : 23.24 % Favored : 72.77 % 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: -0.61 (0.38), residues: 530 helix: 0.14 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.33 (0.50), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 135 HIS 0.009 0.002 HIS A 347 PHE 0.017 0.002 PHE A 385 TYR 0.018 0.001 TYR A 139 ARG 0.002 0.000 ARG A 172 *********************** 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 138 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.404 Fit side-chains REVERT: A 77 ASN cc_start: 0.8404 (m-40) cc_final: 0.8001 (m-40) REVERT: A 200 MET cc_start: 0.6852 (tpt) cc_final: 0.6302 (mmm) REVERT: A 269 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7565 (mm) REVERT: A 283 GLU cc_start: 0.8411 (pp20) cc_final: 0.7801 (pp20) REVERT: A 287 ASP cc_start: 0.7969 (m-30) cc_final: 0.7295 (m-30) REVERT: A 321 ILE cc_start: 0.8238 (pt) cc_final: 0.7953 (pt) REVERT: A 479 ARG cc_start: 0.7512 (ptt180) cc_final: 0.7220 (ptt180) REVERT: A 487 MET cc_start: 0.7085 (tpp) cc_final: 0.5987 (tpp) outliers start: 17 outliers final: 15 residues processed: 124 average time/residue: 0.1425 time to fit residues: 22.8486 Evaluate side-chains 134 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP 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: 0.0770 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3180 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= 0.171 Angle : 0.751 17.976 5883 Z= 0.354 Chirality : 0.041 0.174 642 Planarity : 0.004 0.026 722 Dihedral : 6.736 68.620 585 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.23 % Allowed : 23.94 % Favored : 71.83 % 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: 347 sheet: None (None), residues: 0 loop : -1.28 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 135 HIS 0.009 0.003 HIS A 347 PHE 0.026 0.002 PHE A 404 TYR 0.018 0.001 TYR A 527 ARG 0.002 0.000 ARG A 195 *********************** 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 141 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8398 (m-40) cc_final: 0.7992 (m-40) REVERT: A 121 MET cc_start: 0.8325 (mpp) cc_final: 0.7880 (mpp) REVERT: A 200 MET cc_start: 0.6844 (tpt) cc_final: 0.6299 (mmm) REVERT: A 269 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7581 (mm) REVERT: A 283 GLU cc_start: 0.8394 (pp20) cc_final: 0.7790 (pp20) REVERT: A 287 ASP cc_start: 0.7973 (m-30) cc_final: 0.7278 (m-30) REVERT: A 321 ILE cc_start: 0.8206 (pt) cc_final: 0.7940 (pt) REVERT: A 479 ARG cc_start: 0.7498 (ptt180) cc_final: 0.7212 (ptt180) REVERT: A 486 GLU cc_start: 0.8453 (pp20) cc_final: 0.8245 (pp20) REVERT: A 487 MET cc_start: 0.7055 (tpp) cc_final: 0.5961 (tpp) outliers start: 18 outliers final: 16 residues processed: 126 average time/residue: 0.1382 time to fit residues: 22.6589 Evaluate side-chains 136 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3195 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= 0.169 Angle : 0.746 18.070 5883 Z= 0.354 Chirality : 0.041 0.170 642 Planarity : 0.004 0.025 722 Dihedral : 6.745 68.468 585 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.99 % Allowed : 24.41 % Favored : 71.60 % 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: -0.52 (0.38), residues: 530 helix: 0.22 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.30 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 135 HIS 0.009 0.003 HIS A 347 PHE 0.018 0.002 PHE A 385 TYR 0.018 0.001 TYR A 139 ARG 0.006 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 136 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8419 (m-40) cc_final: 0.7986 (m-40) REVERT: A 200 MET cc_start: 0.6833 (tpt) cc_final: 0.6292 (mmm) REVERT: A 269 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7516 (mm) REVERT: A 283 GLU cc_start: 0.8388 (pp20) cc_final: 0.7775 (pp20) REVERT: A 287 ASP cc_start: 0.7949 (m-30) cc_final: 0.7263 (m-30) REVERT: A 321 ILE cc_start: 0.8190 (pt) cc_final: 0.7926 (pt) REVERT: A 479 ARG cc_start: 0.7456 (ptt180) cc_final: 0.7151 (ptt180) REVERT: A 487 MET cc_start: 0.6944 (tpp) cc_final: 0.5863 (tpp) outliers start: 17 outliers final: 16 residues processed: 124 average time/residue: 0.1288 time to fit residues: 21.0480 Evaluate side-chains 135 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4313 Z= 0.176 Angle : 0.774 18.105 5883 Z= 0.369 Chirality : 0.041 0.166 642 Planarity : 0.004 0.026 722 Dihedral : 6.805 68.126 585 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.23 % Allowed : 25.82 % Favored : 69.95 % 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: -0.49 (0.38), residues: 530 helix: 0.25 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 184 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 0.030 0.001 PHE A 404 TYR 0.032 0.002 TYR A 551 ARG 0.008 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 138 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.8429 (m-40) cc_final: 0.8016 (m-40) REVERT: A 200 MET cc_start: 0.6825 (tpt) cc_final: 0.6447 (mmm) REVERT: A 269 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7469 (mm) REVERT: A 283 GLU cc_start: 0.8393 (pp20) cc_final: 0.7782 (pp20) REVERT: A 287 ASP cc_start: 0.7955 (m-30) cc_final: 0.7272 (m-30) REVERT: A 321 ILE cc_start: 0.8172 (pt) cc_final: 0.7918 (pt) REVERT: A 391 MET cc_start: 0.7907 (mtt) cc_final: 0.7701 (mtt) REVERT: A 487 MET cc_start: 0.6918 (tpp) cc_final: 0.5774 (tpp) outliers start: 18 outliers final: 17 residues processed: 126 average time/residue: 0.1321 time to fit residues: 21.9059 Evaluate side-chains 137 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.162238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139444 restraints weight = 9252.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.143028 restraints weight = 5734.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.145346 restraints weight = 4079.343| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4313 Z= 0.176 Angle : 0.775 18.151 5883 Z= 0.369 Chirality : 0.041 0.164 642 Planarity : 0.004 0.048 722 Dihedral : 6.773 67.833 585 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.23 % Allowed : 25.82 % Favored : 69.95 % 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: -0.35 (0.38), residues: 530 helix: 0.33 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.19 (0.49), residues: 184 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 0.016 0.001 PHE A 385 TYR 0.020 0.001 TYR A 139 ARG 0.007 0.000 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1299.47 seconds wall clock time: 25 minutes 32.71 seconds (1532.71 seconds total)