Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:04:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/04_2023/7sj4_25153.pdb" } resolution = 2.86 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= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2485 2.51 5 N 647 2.21 5 O 754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3909 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2502 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 9, 'TRANS': 294} Chain breaks: 2 Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1383 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 2.53, per 1000 atoms: 0.65 Number of scatterers: 3909 At special positions: 0 Unit cell: (71.28, 82.08, 85.32, 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 23 16.00 O 754 8.00 N 647 7.00 C 2485 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: 1.42 Conformation dependent library (CDL) restraints added in 670.3 milliseconds 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 2 sheets defined 58.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1282 through 1325 removed outlier: 3.685A pdb=" N ALA A1306 " --> pdb=" O GLN A1302 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1319 " --> pdb=" O MET A1315 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP A1320 " --> pdb=" O ASP A1316 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 removed outlier: 3.830A pdb=" N VAL A1334 " --> pdb=" O PRO A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1342 Processing helix chain 'A' and resid 1343 through 1354 removed outlier: 3.547A pdb=" N ASN A1353 " --> pdb=" O GLU A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1362 removed outlier: 3.687A pdb=" N TYR A1362 " --> pdb=" O GLU A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1367 No H-bonds generated for 'chain 'A' and resid 1365 through 1367' Processing helix chain 'A' and resid 1368 through 1376 removed outlier: 4.122A pdb=" N CYS A1372 " --> pdb=" O ASP A1368 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A1373 " --> pdb=" O VAL A1369 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP A1376 " --> pdb=" O CYS A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1379 No H-bonds generated for 'chain 'A' and resid 1377 through 1379' Processing helix chain 'A' and resid 1380 through 1398 removed outlier: 3.883A pdb=" N VAL A1384 " --> pdb=" O PHE A1380 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Proline residue: A1391 - end of helix removed outlier: 3.596A pdb=" N GLN A1395 " --> pdb=" O PRO A1391 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1396 " --> pdb=" O ASP A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1413 Processing helix chain 'A' and resid 1417 through 1423 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.754A pdb=" N THR A1430 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1441 Processing helix chain 'A' and resid 1446 through 1471 removed outlier: 3.522A pdb=" N ILE A1450 " --> pdb=" O GLY A1446 " (cutoff:3.500A) Proline residue: A1461 - end of helix Processing helix chain 'A' and resid 1480 through 1484 Processing helix chain 'A' and resid 1575 through 1594 Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.572A pdb=" N TYR B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.568A pdb=" N SER B 71 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.626A pdb=" N PHE B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.533A pdb=" N GLU B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.710A pdb=" N LYS B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 164 through 177 removed outlier: 4.089A pdb=" N PHE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1473 through 1474 removed outlier: 3.571A pdb=" N LYS A1530 " --> pdb=" O VAL A1522 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A1518 " --> pdb=" O LYS A1534 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1536 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A1516 " --> pdb=" O LYS A1536 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1515 " --> pdb=" O PHE A1512 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU A1521 " --> pdb=" O GLU A1506 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU A1506 " --> pdb=" O GLU A1521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A1492 " --> pdb=" O ARG A1507 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A1488 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1493 " --> pdb=" O LYS A1572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1570 " --> pdb=" O TRP A1495 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.721A pdb=" N VAL B 46 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN B 2 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 78 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 80 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR B 115 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 82 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE B 110 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N LEU B 155 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 112 " --> pdb=" O LEU B 155 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 573 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: 0.99 Time building geometry restraints manager: 1.56 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: 1254 1.34 - 1.46: 812 1.46 - 1.58: 1863 1.58 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3964 Sorted by residual: bond pdb=" C GLY A1504 " pdb=" O GLY A1504 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.62e-01 bond pdb=" C ARG B 68 " pdb=" N PRO B 69 " ideal model delta sigma weight residual 1.334 1.349 -0.016 2.34e-02 1.83e+03 4.44e-01 bond pdb=" C TYR B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 1.332 1.340 -0.008 1.30e-02 5.92e+03 3.87e-01 bond pdb=" CA ASP A1551 " pdb=" C ASP A1551 " ideal model delta sigma weight residual 1.517 1.523 -0.006 1.07e-02 8.73e+03 3.30e-01 bond pdb=" CA ILE A1301 " pdb=" C ILE A1301 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.30e-02 5.92e+03 2.98e-01 ... (remaining 3959 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 128 107.29 - 113.96: 2237 113.96 - 120.63: 1633 120.63 - 127.31: 1309 127.31 - 133.98: 43 Bond angle restraints: 5350 Sorted by residual: angle pdb=" N TYR B 72 " pdb=" CA TYR B 72 " pdb=" C TYR B 72 " ideal model delta sigma weight residual 109.81 114.15 -4.34 2.21e+00 2.05e-01 3.85e+00 angle pdb=" N GLY A1504 " pdb=" CA GLY A1504 " pdb=" C GLY A1504 " ideal model delta sigma weight residual 110.97 113.51 -2.54 1.56e+00 4.11e-01 2.65e+00 angle pdb=" CA TYR B 72 " pdb=" C TYR B 72 " pdb=" N PRO B 73 " ideal model delta sigma weight residual 118.44 120.56 -2.12 1.59e+00 3.96e-01 1.78e+00 angle pdb=" N ILE A1354 " pdb=" CA ILE A1354 " pdb=" C ILE A1354 " ideal model delta sigma weight residual 109.34 111.93 -2.59 2.08e+00 2.31e-01 1.56e+00 angle pdb=" C VAL A1460 " pdb=" N PRO A1461 " pdb=" CD PRO A1461 " ideal model delta sigma weight residual 125.00 130.00 -5.00 4.10e+00 5.95e-02 1.49e+00 ... (remaining 5345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.43: 2180 11.43 - 22.86: 169 22.86 - 34.29: 43 34.29 - 45.72: 15 45.72 - 57.15: 5 Dihedral angle restraints: 2412 sinusoidal: 1006 harmonic: 1406 Sorted by residual: dihedral pdb=" CA MET A1457 " pdb=" C MET A1457 " pdb=" N LEU A1458 " pdb=" CA LEU A1458 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" N LYS B 166 " pdb=" CA LYS B 166 " pdb=" CB LYS B 166 " pdb=" CG LYS B 166 " ideal model delta sinusoidal sigma weight residual -60.00 -117.15 57.15 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ARG A1505 " pdb=" CB ARG A1505 " pdb=" CG ARG A1505 " pdb=" CD ARG A1505 " ideal model delta sinusoidal sigma weight residual 60.00 115.55 -55.55 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 340 0.026 - 0.053: 147 0.053 - 0.079: 65 0.079 - 0.105: 29 0.105 - 0.132: 12 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA ILE A1329 " pdb=" N ILE A1329 " pdb=" C ILE A1329 " pdb=" CB ILE A1329 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA LYS A1424 " pdb=" N LYS A1424 " pdb=" C LYS A1424 " pdb=" CB LYS A1424 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE B 111 " pdb=" N ILE B 111 " pdb=" C ILE B 111 " pdb=" CB ILE B 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 590 not shown) Planarity restraints: 681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1329 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A1330 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A1330 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1330 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 135 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO B 136 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 68 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO B 69 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.014 5.00e-02 4.00e+02 ... (remaining 678 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 959 2.80 - 3.33: 3554 3.33 - 3.85: 6215 3.85 - 4.38: 7413 4.38 - 4.90: 12867 Nonbonded interactions: 31008 Sorted by model distance: nonbonded pdb=" NE2 HIS A1351 " pdb=" OH TYR A1383 " model vdw 2.278 2.520 nonbonded pdb=" OD1 ASN B 39 " pdb=" O HOH B 201 " model vdw 2.283 2.440 nonbonded pdb=" O GLY B 10 " pdb=" O HOH B 202 " model vdw 2.298 2.440 nonbonded pdb=" O ASP B 57 " pdb=" O HOH B 203 " model vdw 2.307 2.440 nonbonded pdb=" O THR B 35 " pdb=" O HOH B 204 " model vdw 2.308 2.440 ... (remaining 31003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.110 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.002 0.018 3964 Z= 0.133 Angle : 0.432 5.003 5350 Z= 0.234 Chirality : 0.041 0.132 593 Planarity : 0.003 0.032 681 Dihedral : 9.562 57.150 1502 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.40), residues: 473 helix: 1.15 (0.35), residues: 239 sheet: 0.12 (0.52), residues: 89 loop : 0.34 (0.55), residues: 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 1.2826 time to fit residues: 134.8046 Evaluate side-chains 72 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1352 ASN A1353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3964 Z= 0.202 Angle : 0.537 5.109 5350 Z= 0.291 Chirality : 0.043 0.162 593 Planarity : 0.004 0.034 681 Dihedral : 3.954 16.014 517 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.02 % 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: 1.26 (0.39), residues: 473 helix: 1.55 (0.34), residues: 236 sheet: 0.20 (0.52), residues: 89 loop : 0.25 (0.52), residues: 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.356 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 79 average time/residue: 0.9983 time to fit residues: 81.5461 Evaluate side-chains 70 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.5518 time to fit residues: 1.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3964 Z= 0.173 Angle : 0.519 6.384 5350 Z= 0.274 Chirality : 0.043 0.173 593 Planarity : 0.004 0.036 681 Dihedral : 3.924 15.568 517 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.71 % 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: 1.39 (0.39), residues: 473 helix: 1.77 (0.34), residues: 236 sheet: 0.24 (0.52), residues: 91 loop : 0.11 (0.52), residues: 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.473 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 75 average time/residue: 1.1832 time to fit residues: 91.8186 Evaluate side-chains 67 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6110 time to fit residues: 1.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 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: 0.7046 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3964 Z= 0.190 Angle : 0.517 6.719 5350 Z= 0.269 Chirality : 0.043 0.151 593 Planarity : 0.004 0.039 681 Dihedral : 3.929 16.787 517 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 2.55 % 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: 1.47 (0.39), residues: 473 helix: 1.87 (0.34), residues: 237 sheet: 0.22 (0.53), residues: 91 loop : 0.13 (0.53), residues: 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.390 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 1.0218 time to fit residues: 75.1655 Evaluate side-chains 69 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.6822 time to fit residues: 3.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7061 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3964 Z= 0.211 Angle : 0.545 6.804 5350 Z= 0.280 Chirality : 0.043 0.137 593 Planarity : 0.004 0.038 681 Dihedral : 3.983 17.598 517 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 3.02 % 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: 1.42 (0.39), residues: 473 helix: 1.83 (0.34), residues: 237 sheet: 0.21 (0.53), residues: 91 loop : 0.08 (0.52), residues: 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.507 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 1.0995 time to fit residues: 77.6121 Evaluate side-chains 67 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4274 time to fit residues: 2.0749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7048 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3964 Z= 0.184 Angle : 0.527 6.930 5350 Z= 0.272 Chirality : 0.042 0.136 593 Planarity : 0.004 0.033 681 Dihedral : 3.964 17.509 517 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.71 % 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: 1.57 (0.39), residues: 473 helix: 2.00 (0.34), residues: 237 sheet: 0.17 (0.53), residues: 91 loop : 0.15 (0.53), residues: 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.472 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 1.1773 time to fit residues: 84.2212 Evaluate side-chains 68 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.6490 time to fit residues: 4.0762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3964 Z= 0.198 Angle : 0.524 8.480 5350 Z= 0.270 Chirality : 0.043 0.138 593 Planarity : 0.004 0.041 681 Dihedral : 3.951 17.229 517 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.94 % 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: 1.58 (0.39), residues: 473 helix: 1.97 (0.34), residues: 238 sheet: 0.17 (0.54), residues: 91 loop : 0.20 (0.53), residues: 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.474 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 71 average time/residue: 1.1578 time to fit residues: 85.1710 Evaluate side-chains 66 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.3315 time to fit residues: 2.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.7045 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3964 Z= 0.190 Angle : 0.550 9.923 5350 Z= 0.281 Chirality : 0.042 0.132 593 Planarity : 0.004 0.039 681 Dihedral : 3.897 16.564 517 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 2.55 % 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: 1.69 (0.39), residues: 473 helix: 2.09 (0.34), residues: 238 sheet: 0.18 (0.54), residues: 91 loop : 0.23 (0.54), residues: 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.489 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 1.1716 time to fit residues: 80.1543 Evaluate side-chains 66 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.3949 time to fit residues: 1.9391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7058 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3964 Z= 0.210 Angle : 0.565 10.693 5350 Z= 0.291 Chirality : 0.042 0.135 593 Planarity : 0.004 0.037 681 Dihedral : 3.953 16.279 517 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 1.55 (0.39), residues: 473 helix: 1.93 (0.34), residues: 237 sheet: 0.17 (0.54), residues: 91 loop : 0.24 (0.53), residues: 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.475 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 1.1301 time to fit residues: 71.6513 Evaluate side-chains 58 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1774 time to fit residues: 0.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7056 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3964 Z= 0.217 Angle : 0.580 11.834 5350 Z= 0.298 Chirality : 0.042 0.136 593 Planarity : 0.004 0.037 681 Dihedral : 3.950 15.963 517 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 2.09 % 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: 1.53 (0.40), residues: 473 helix: 1.92 (0.34), residues: 237 sheet: 0.16 (0.54), residues: 91 loop : 0.20 (0.54), residues: 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 946 Ramachandran restraints generated. 473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.440 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 1.0971 time to fit residues: 68.4094 Evaluate side-chains 61 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4240 time to fit residues: 1.9857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156614 restraints weight = 4032.627| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.34 r_work: 0.3794 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3964 Z= 0.199 Angle : 0.568 12.073 5350 Z= 0.292 Chirality : 0.042 0.134 593 Planarity : 0.004 0.036 681 Dihedral : 3.917 16.271 517 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.62 % 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: 1.57 (0.40), residues: 473 helix: 1.96 (0.34), residues: 237 sheet: 0.18 (0.54), residues: 91 loop : 0.22 (0.54), residues: 145 =============================================================================== Job complete usr+sys time: 1947.81 seconds wall clock time: 35 minutes 40.78 seconds (2140.78 seconds total)