Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:48:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c03_16354/04_2023/8c03_16354_updated.pdb" } resolution = 3.89 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= 0.001 sd= 0.028 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2187 2.51 5 N 542 2.21 5 O 574 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3330 Unusual residues: {'SZU': 1} Classifications: {'peptide': 429, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 419, None: 1} Not linked: pdbres="LYS A 549 " pdbres="SZU A 601 " Chain breaks: 2 Time building chain proxies: 2.29, per 1000 atoms: 0.69 Number of scatterers: 3330 At special positions: 0 Unit cell: (78.12, 67.704, 84.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 F 1 9.00 O 574 8.00 N 542 7.00 C 2187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 490.6 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 53 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.634A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 126 through 155 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.742A pdb=" N GLY A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 486 through 513 removed outlier: 3.690A pdb=" N ARG A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 493 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 545 279 hydrogen bonds defined for protein. 777 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: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1028 1.34 - 1.46: 824 1.46 - 1.58: 1505 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 3401 Sorted by residual: bond pdb=" C1 SZU A 601 " pdb=" C8 SZU A 601 " ideal model delta sigma weight residual 1.532 1.325 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.526 1.377 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C1 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 1.463 1.329 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C7 SZU A 601 " pdb=" F1 SZU A 601 " ideal model delta sigma weight residual 1.415 1.292 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C9 SZU A 601 " pdb=" O2 SZU A 601 " ideal model delta sigma weight residual 1.287 1.405 -0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.55: 75 106.55 - 113.40: 1952 113.40 - 120.25: 1289 120.25 - 127.10: 1271 127.10 - 133.95: 40 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N4 SZU A 601 " ideal model delta sigma weight residual 145.49 125.60 19.89 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N5 SZU A 601 " ideal model delta sigma weight residual 105.25 124.12 -18.87 3.00e+00 1.11e-01 3.96e+01 angle pdb=" N GLN A 496 " pdb=" CA GLN A 496 " pdb=" C GLN A 496 " ideal model delta sigma weight residual 111.36 106.91 4.45 1.09e+00 8.42e-01 1.67e+01 angle pdb=" N LEU A 59 " pdb=" CA LEU A 59 " pdb=" C LEU A 59 " ideal model delta sigma weight residual 111.11 106.50 4.61 1.20e+00 6.94e-01 1.48e+01 angle pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" O THR A 334 " ideal model delta sigma weight residual 120.90 117.00 3.90 1.03e+00 9.43e-01 1.43e+01 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 1897 28.00 - 56.01: 58 56.01 - 84.01: 4 84.01 - 112.01: 0 112.01 - 140.01: 1 Dihedral angle restraints: 1960 sinusoidal: 731 harmonic: 1229 Sorted by residual: dihedral pdb=" C13 SZU A 601 " pdb=" C14 SZU A 601 " pdb=" C15 SZU A 601 " pdb=" N5 SZU A 601 " ideal model delta sinusoidal sigma weight residual 196.57 56.56 140.01 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" N GLU A 518 " pdb=" CA GLU A 518 " pdb=" CB GLU A 518 " pdb=" CG GLU A 518 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sinusoidal sigma weight residual 180.00 123.89 56.11 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 1957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 473 0.052 - 0.104: 74 0.104 - 0.156: 9 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA LEU A 59 " pdb=" N LEU A 59 " pdb=" C LEU A 59 " pdb=" CB LEU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 333 " pdb=" N TYR A 333 " pdb=" C TYR A 333 " pdb=" CB TYR A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 324 " pdb=" N PHE A 324 " pdb=" C PHE A 324 " pdb=" CB PHE A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 557 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A 53 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 53 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 54 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 324 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C PHE A 324 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 324 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 325 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 SZU A 601 " -0.004 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C2 SZU A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C8 SZU A 601 " 0.013 2.00e-02 2.50e+03 pdb=" N1 SZU A 601 " -0.023 2.00e-02 2.50e+03 pdb=" O1 SZU A 601 " -0.002 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 1 1.97 - 2.70: 83 2.70 - 3.43: 5442 3.43 - 4.17: 7372 4.17 - 4.90: 13869 Nonbonded interactions: 26767 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 2.440 nonbonded pdb=" CD1 LEU A 469 " pdb=" F1 SZU A 601 " model vdw 2.141 3.410 nonbonded pdb=" O TYR A 20 " pdb=" OG SER A 23 " model vdw 2.205 2.440 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 2.520 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 2.440 ... (remaining 26762 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: 0.390 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: 1.510 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.008 0.207 3401 Z= 0.473 Angle : 0.802 19.886 4627 Z= 0.429 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 13.065 140.014 1172 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 3.06 % 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: 2.75 (0.41), residues: 423 helix: 2.29 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -0.88 (0.85), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1399 time to fit residues: 23.5576 Evaluate side-chains 104 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0323 time to fit residues: 0.5710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 194 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3401 Z= 0.188 Angle : 0.560 8.062 4627 Z= 0.288 Chirality : 0.037 0.125 560 Planarity : 0.004 0.025 556 Dihedral : 7.286 120.392 464 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.40), residues: 423 helix: 2.23 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.11 (0.98), residues: 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 114 average time/residue: 0.1255 time to fit residues: 17.9822 Evaluate side-chains 102 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0354 time to fit residues: 0.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 3401 Z= 0.317 Angle : 0.639 8.243 4627 Z= 0.325 Chirality : 0.039 0.158 560 Planarity : 0.004 0.021 556 Dihedral : 7.274 117.868 464 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 4.18 % 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: 2.46 (0.41), residues: 423 helix: 1.93 (0.26), residues: 365 sheet: None (None), residues: 0 loop : -0.19 (0.97), residues: 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.357 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.1265 time to fit residues: 17.4066 Evaluate side-chains 108 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0346 time to fit residues: 1.1688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3401 Z= 0.255 Angle : 0.605 9.359 4627 Z= 0.306 Chirality : 0.038 0.157 560 Planarity : 0.004 0.028 556 Dihedral : 7.325 114.957 464 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 2.23 % 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: 2.42 (0.41), residues: 423 helix: 2.00 (0.26), residues: 361 sheet: None (None), residues: 0 loop : -0.70 (0.90), residues: 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.397 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.1356 time to fit residues: 17.5690 Evaluate side-chains 102 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0325 time to fit residues: 0.7681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.203 Angle : 0.591 10.288 4627 Z= 0.297 Chirality : 0.038 0.146 560 Planarity : 0.004 0.029 556 Dihedral : 7.216 109.271 464 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.41), residues: 423 helix: 2.04 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.67 (0.93), residues: 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.381 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 105 average time/residue: 0.1292 time to fit residues: 17.1270 Evaluate side-chains 96 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0375 time to fit residues: 0.5918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3401 Z= 0.224 Angle : 0.644 10.917 4627 Z= 0.317 Chirality : 0.039 0.188 560 Planarity : 0.003 0.023 556 Dihedral : 7.151 106.986 464 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.41), residues: 423 helix: 1.92 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.72 (0.91), residues: 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.377 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 0.1321 time to fit residues: 16.2636 Evaluate side-chains 96 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0486 time to fit residues: 0.9632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3401 Z= 0.237 Angle : 0.645 11.116 4627 Z= 0.318 Chirality : 0.038 0.179 560 Planarity : 0.003 0.024 556 Dihedral : 7.093 104.775 464 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.11 % 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: 2.28 (0.41), residues: 423 helix: 1.86 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.66 (0.92), residues: 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.413 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 98 average time/residue: 0.1252 time to fit residues: 15.3836 Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0345 time to fit residues: 0.6908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.221 Angle : 0.643 10.507 4627 Z= 0.316 Chirality : 0.038 0.178 560 Planarity : 0.003 0.022 556 Dihedral : 6.989 101.210 464 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.41), residues: 423 helix: 1.86 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.64 (0.92), residues: 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.389 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.1347 time to fit residues: 16.2737 Evaluate side-chains 97 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0395 time to fit residues: 0.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.226 Angle : 0.655 11.232 4627 Z= 0.321 Chirality : 0.038 0.179 560 Planarity : 0.003 0.023 556 Dihedral : 6.849 97.868 464 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.42), residues: 423 helix: 1.92 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.63 (0.92), residues: 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.390 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.1298 time to fit residues: 15.8202 Evaluate side-chains 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0337 time to fit residues: 0.5365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3401 Z= 0.236 Angle : 0.653 9.135 4627 Z= 0.322 Chirality : 0.038 0.175 560 Planarity : 0.003 0.023 556 Dihedral : 6.753 94.348 464 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.11 % 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: 2.28 (0.42), residues: 423 helix: 1.86 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -0.69 (0.92), residues: 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.338 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.1345 time to fit residues: 15.3702 Evaluate side-chains 91 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0358 time to fit residues: 0.6900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 22 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131344 restraints weight = 4858.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135374 restraints weight = 3130.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138121 restraints weight = 2374.183| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3401 Z= 0.210 Angle : 0.667 9.291 4627 Z= 0.328 Chirality : 0.039 0.177 560 Planarity : 0.003 0.025 556 Dihedral : 6.588 88.958 464 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.56 % 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: 2.30 (0.42), residues: 423 helix: 1.89 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.62 (0.90), residues: 60 =============================================================================== Job complete usr+sys time: 1017.57 seconds wall clock time: 19 minutes 2.91 seconds (1142.91 seconds total)