Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:03:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/11_2022/7sj4_25153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/11_2022/7sj4_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_25153/11_2022/7sj4_25153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/11_2022/7sj4_25153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/11_2022/7sj4_25153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj4_25153/11_2022/7sj4_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 Convert atoms to be neutral 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-dev-4778/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: 2.92, per 1000 atoms: 0.75 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: 1.52 Conformation dependent library (CDL) restraints added in 722.8 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: 1.05 Time building geometry restraints manager: 1.66 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 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. 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: 0.400 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: 2.160 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.940 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 3.73 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 : 0.452 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 1.1753 time to fit residues: 123.5958 Evaluate side-chains 72 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5831 ------------------------------------------------------------------------------- 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: 0.7283 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 5.103 5350 Z= 0.291 Chirality : 0.043 0.162 593 Planarity : 0.004 0.034 681 Dihedral : 3.954 16.010 517 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.30 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 : 0.481 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 79 average time/residue: 1.1256 time to fit residues: 92.4099 Evaluate side-chains 70 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6552 time to fit residues: 2.0636 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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: 0.7246 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3964 Z= 0.166 Angle : 0.514 6.345 5350 Z= 0.271 Chirality : 0.042 0.176 593 Planarity : 0.004 0.036 681 Dihedral : 3.895 15.442 517 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 1.45 (0.39), residues: 473 helix: 1.82 (0.34), residues: 236 sheet: 0.26 (0.52), residues: 91 loop : 0.15 (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: 17 poor density : 63 time to evaluate : 0.537 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 75 average time/residue: 1.0856 time to fit residues: 84.4483 Evaluate side-chains 66 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.5963 time to fit residues: 1.9477 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7270 moved from start: 0.2563 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= 0.191 Angle : 0.518 6.762 5350 Z= 0.270 Chirality : 0.043 0.154 593 Planarity : 0.004 0.039 681 Dihedral : 3.909 16.805 517 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 2.32 % 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: 1.54 (0.39), residues: 473 helix: 1.97 (0.34), residues: 236 sheet: 0.25 (0.53), residues: 91 loop : 0.09 (0.53), residues: 146 *********************** 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 73 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.502 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 1.0273 time to fit residues: 73.8725 Evaluate side-chains 67 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.6486 time to fit residues: 3.4193 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7272 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3964 Z= 0.188 Angle : 0.531 6.940 5350 Z= 0.273 Chirality : 0.043 0.135 593 Planarity : 0.004 0.037 681 Dihedral : 3.922 17.742 517 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.30 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: 1.58 (0.39), residues: 473 helix: 2.02 (0.34), residues: 236 sheet: 0.25 (0.53), residues: 91 loop : 0.07 (0.53), residues: 146 *********************** 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 : 0.514 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 67 average time/residue: 1.0613 time to fit residues: 73.9574 Evaluate side-chains 62 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4228 time to fit residues: 2.0595 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3964 Z= 0.192 Angle : 0.521 6.691 5350 Z= 0.268 Chirality : 0.043 0.137 593 Planarity : 0.004 0.034 681 Dihedral : 3.962 17.142 517 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.25 % 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: 1.59 (0.39), residues: 473 helix: 2.03 (0.34), residues: 236 sheet: 0.15 (0.53), residues: 91 loop : 0.17 (0.53), residues: 146 *********************** 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 73 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.504 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 1.1398 time to fit residues: 79.3364 Evaluate side-chains 68 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.0122 time to fit residues: 5.0810 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.2790 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= 0.208 Angle : 0.544 7.133 5350 Z= 0.282 Chirality : 0.043 0.138 593 Planarity : 0.004 0.032 681 Dihedral : 3.981 16.618 517 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 2.78 % 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: 1.62 (0.39), residues: 473 helix: 2.07 (0.34), residues: 235 sheet: 0.16 (0.53), residues: 91 loop : 0.18 (0.53), residues: 147 *********************** 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 72 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.450 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 1.0027 time to fit residues: 68.9946 Evaluate side-chains 64 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.3636 time to fit residues: 2.3172 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 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: 0.7283 moved from start: 0.2803 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= 0.206 Angle : 0.546 9.021 5350 Z= 0.281 Chirality : 0.042 0.136 593 Planarity : 0.004 0.033 681 Dihedral : 3.947 16.082 517 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.94 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: 1.63 (0.39), residues: 473 helix: 2.08 (0.34), residues: 236 sheet: 0.18 (0.53), residues: 91 loop : 0.14 (0.53), residues: 146 *********************** 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 69 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.519 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.9682 time to fit residues: 62.7507 Evaluate side-chains 65 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.3265 time to fit residues: 2.1109 ------------------------------------------------------------------------------- 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: 0.9980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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: 0.7278 moved from start: 0.2846 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= 0.194 Angle : 0.544 10.357 5350 Z= 0.279 Chirality : 0.042 0.133 593 Planarity : 0.004 0.032 681 Dihedral : 3.927 16.037 517 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 2.78 % 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: 1.64 (0.39), residues: 473 helix: 2.07 (0.34), residues: 236 sheet: 0.18 (0.54), residues: 91 loop : 0.18 (0.53), residues: 146 *********************** 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 68 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.510 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 62 average time/residue: 1.0336 time to fit residues: 66.7780 Evaluate side-chains 60 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.7840 time to fit residues: 2.3189 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3964 Z= 0.220 Angle : 0.573 11.019 5350 Z= 0.295 Chirality : 0.042 0.136 593 Planarity : 0.004 0.032 681 Dihedral : 3.973 15.975 517 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 1.55 (0.40), residues: 473 helix: 1.93 (0.34), residues: 237 sheet: 0.16 (0.54), residues: 91 loop : 0.23 (0.53), 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 64 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.484 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 1.0104 time to fit residues: 64.2183 Evaluate side-chains 60 residues out of total 431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.5834 time to fit residues: 1.8977 ------------------------------------------------------------------------------- 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: 0.6980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.0470 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.194647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158816 restraints weight = 4023.354| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.33 r_work: 0.3893 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3871 rms_B_bonded: 2.16 restraints_weight: 0.1250 r_work: 0.3859 rms_B_bonded: 2.24 restraints_weight: 0.0625 r_work: 0.3846 rms_B_bonded: 2.36 restraints_weight: 0.0312 r_work: 0.3833 rms_B_bonded: 2.50 restraints_weight: 0.0156 r_work: 0.3819 rms_B_bonded: 2.68 restraints_weight: 0.0078 r_work: 0.3803 rms_B_bonded: 2.88 restraints_weight: 0.0039 r_work: 0.3787 rms_B_bonded: 3.12 restraints_weight: 0.0020 r_work: 0.3770 rms_B_bonded: 3.39 restraints_weight: 0.0010 r_work: 0.3751 rms_B_bonded: 3.69 restraints_weight: 0.0005 r_work: 0.3731 rms_B_bonded: 4.04 restraints_weight: 0.0002 r_work: 0.3709 rms_B_bonded: 4.43 restraints_weight: 0.0001 r_work: 0.3686 rms_B_bonded: 4.86 restraints_weight: 0.0001 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2907 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= 0.195 Angle : 0.569 11.837 5350 Z= 0.293 Chirality : 0.042 0.133 593 Planarity : 0.004 0.031 681 Dihedral : 3.915 16.002 517 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 1.55 (0.40), residues: 473 helix: 1.92 (0.34), residues: 238 sheet: 0.19 (0.54), residues: 91 loop : 0.22 (0.54), residues: 144 =============================================================================== Job complete usr+sys time: 1815.05 seconds wall clock time: 33 minutes 1.50 seconds (1981.50 seconds total)