Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:21:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_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_25170/11_2022/7sk2_25170_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk2_25170/11_2022/7sk2_25170_updated.pdb" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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: 2.95, per 1000 atoms: 0.71 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: 1.74 Conformation dependent library (CDL) restraints added in 585.4 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: 3.77 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: 0.91 Time building geometry restraints manager: 1.90 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 1.597 1.430 0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C02 TGI A 601 " pdb=" C06 TGI A 601 " ideal model delta sigma weight residual 1.596 1.433 0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" C03 TGI A 601 " pdb=" S04 TGI A 601 " ideal model delta sigma weight residual 1.555 1.690 -0.135 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C23 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.555 1.688 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C20 TGI A 601 " pdb=" S24 TGI A 601 " ideal model delta sigma weight residual 1.555 1.687 -0.132 2.00e-02 2.50e+03 4.38e+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=" 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 angle pdb=" C SER A 302 " pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C LEU A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta sigma weight residual 122.06 115.23 6.83 1.86e+00 2.89e-01 1.35e+01 ... (remaining 5878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 2193 16.93 - 33.86: 177 33.86 - 50.80: 40 50.80 - 67.73: 5 67.73 - 84.66: 4 Dihedral angle restraints: 2419 sinusoidal: 889 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 2416 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 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. 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: 0.810 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: 3.700 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 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 0.167 4313 Z= 0.500 Angle : 1.053 10.959 5883 Z= 0.543 Chirality : 0.055 0.197 642 Planarity : 0.006 0.044 722 Dihedral : 13.596 84.661 1444 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 % 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 *********************** 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 : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1338 time to fit residues: 23.2597 Evaluate side-chains 110 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6368 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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: 0.6970 moved from start: 0.1690 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= 0.180 Angle : 0.660 6.493 5883 Z= 0.338 Chirality : 0.041 0.128 642 Planarity : 0.004 0.033 722 Dihedral : 6.417 58.030 582 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.36), residues: 530 helix: -0.64 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 178 *********************** 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 131 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.495 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 125 average time/residue: 0.1306 time to fit residues: 21.5727 Evaluate side-chains 120 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0415 time to fit residues: 1.2281 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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: 0.6987 moved from start: 0.2191 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= 0.181 Angle : 0.641 6.977 5883 Z= 0.326 Chirality : 0.041 0.130 642 Planarity : 0.004 0.029 722 Dihedral : 6.279 59.406 582 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.17 % 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: -0.38 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -1.77 (0.50), residues: 166 *********************** 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: 5 poor density : 120 time to evaluate : 0.479 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 122 average time/residue: 0.1301 time to fit residues: 20.8782 Evaluate side-chains 116 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0484 time to fit residues: 0.9643 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 A 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4313 Z= 0.163 Angle : 0.627 7.868 5883 Z= 0.318 Chirality : 0.040 0.120 642 Planarity : 0.004 0.027 722 Dihedral : 6.130 59.967 582 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 2.35 % 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: -0.80 (0.38), residues: 530 helix: 0.01 (0.28), residues: 354 sheet: None (None), residues: 0 loop : -1.50 (0.50), residues: 176 *********************** 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 132 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.500 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.1350 time to fit residues: 21.9875 Evaluate side-chains 121 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0435 time to fit residues: 1.0925 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7015 moved from start: 0.2763 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= 0.196 Angle : 0.642 8.364 5883 Z= 0.325 Chirality : 0.041 0.170 642 Planarity : 0.004 0.027 722 Dihedral : 6.047 59.592 582 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.17 % 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: 0.07 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.38 (0.51), residues: 177 *********************** 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 124 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.435 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 120 average time/residue: 0.1251 time to fit residues: 20.1971 Evaluate side-chains 117 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0437 time to fit residues: 0.9807 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 0.0040 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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: 0.7022 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4313 Z= 0.199 Angle : 0.637 6.379 5883 Z= 0.326 Chirality : 0.041 0.163 642 Planarity : 0.004 0.026 722 Dihedral : 6.002 59.444 582 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.38), residues: 530 helix: 0.11 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.35 (0.51), residues: 178 *********************** 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 127 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.459 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 124 average time/residue: 0.1316 time to fit residues: 21.6938 Evaluate side-chains 119 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0445 time to fit residues: 0.9861 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4313 Z= 0.186 Angle : 0.671 9.314 5883 Z= 0.338 Chirality : 0.041 0.151 642 Planarity : 0.004 0.026 722 Dihedral : 6.077 59.548 582 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.94 % 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: -0.60 (0.38), residues: 530 helix: 0.16 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.40 (0.51), residues: 177 *********************** 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 123 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.477 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1249 time to fit residues: 19.9142 Evaluate side-chains 118 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0553 time to fit residues: 1.0058 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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: 0.6953 moved from start: 0.3214 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= 0.164 Angle : 0.675 9.654 5883 Z= 0.337 Chirality : 0.041 0.146 642 Planarity : 0.004 0.026 722 Dihedral : 6.025 59.586 582 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.41 % 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: -0.53 (0.38), residues: 530 helix: 0.24 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.42 (0.50), residues: 179 *********************** 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 126 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.501 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.1216 time to fit residues: 19.6569 Evaluate side-chains 123 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0432 time to fit residues: 1.0623 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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: 0.6941 moved from start: 0.3277 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= 0.173 Angle : 0.680 9.979 5883 Z= 0.341 Chirality : 0.041 0.173 642 Planarity : 0.004 0.026 722 Dihedral : 6.021 59.379 582 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.47 % 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: -0.55 (0.38), residues: 530 helix: 0.17 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.35 (0.51), residues: 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: 2 poor density : 119 time to evaluate : 0.577 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.1241 time to fit residues: 19.9883 Evaluate side-chains 121 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0435 time to fit residues: 0.8070 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3324 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= 0.188 Angle : 0.700 10.566 5883 Z= 0.353 Chirality : 0.042 0.175 642 Planarity : 0.004 0.025 722 Dihedral : 6.032 59.292 582 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.41 % 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: 0.05 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.42 (0.51), residues: 166 ********************** 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 126 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.475 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.1259 time to fit residues: 20.2381 Evaluate side-chains 123 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0446 time to fit residues: 0.7812 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.162363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139978 restraints weight = 9241.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.143580 restraints weight = 5729.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.145731 restraints weight = 4054.244| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3461 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= 0.184 Angle : 0.682 10.130 5883 Z= 0.343 Chirality : 0.043 0.179 642 Planarity : 0.004 0.026 722 Dihedral : 6.041 58.990 582 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.47 % 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: 0.08 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.32 (0.51), residues: 171 =============================================================================== Job complete usr+sys time: 1207.96 seconds wall clock time: 23 minutes 3.49 seconds (1383.49 seconds total)