Starting phenix.real_space_refine on Wed Mar 5 22:34:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_25153.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_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/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_25153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_25153.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_25153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2025/7sj4_25153.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.108 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. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.09, per 1000 atoms: 0.79 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 - 3.00 Amino acid : True - 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: 0.93 Conformation dependent library (CDL) restraints added in 463.3 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: 0.46 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: 1.20 Time building geometry restraints manager: 1.13 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: 0.00 - 1.00: 5189 1.00 - 2.00: 131 2.00 - 3.00: 20 3.00 - 4.00: 2 4.00 - 5.00: 8 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 3.120 nonbonded pdb=" OD1 ASN B 39 " pdb=" O HOH B 201 " model vdw 2.283 3.040 nonbonded pdb=" O GLY B 10 " pdb=" O HOH B 202 " model vdw 2.298 3.040 nonbonded pdb=" O ASP B 57 " pdb=" O HOH B 203 " model vdw 2.307 3.040 nonbonded pdb=" O THR B 35 " pdb=" O HOH B 204 " model vdw 2.308 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.620 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- 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 % Allowed : 2.09 % Favored : 96.98 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 97 HIS 0.002 0.000 HIS A1508 PHE 0.011 0.001 PHE A1518 TYR 0.011 0.001 TYR A1404 ARG 0.002 0.000 ARG B 68 *********************** 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 to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 1352 ASN cc_start: 0.8470 (t0) cc_final: 0.7964 (t0) REVERT: A 1389 ASN cc_start: 0.7254 (t0) cc_final: 0.7044 (t0) REVERT: A 1479 ASN cc_start: 0.7846 (m-40) cc_final: 0.7319 (p0) REVERT: A 1505 ARG cc_start: 0.7473 (mpp80) cc_final: 0.7030 (mtp180) REVERT: A 1588 GLU cc_start: 0.8095 (tp30) cc_final: 0.7846 (tp30) REVERT: B 107 ASN cc_start: 0.7677 (m-40) cc_final: 0.7399 (m-40) REVERT: B 120 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5397 (ttt-90) REVERT: B 128 LYS cc_start: 0.8000 (mttt) cc_final: 0.7675 (mptt) REVERT: B 156 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8261 (mt-10) outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 1.2452 time to fit residues: 130.8868 Evaluate side-chains 75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 120 ARG 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: 4.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.194005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.158532 restraints weight = 4006.865| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.26 r_work: 0.3834 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3964 Z= 0.199 Angle : 0.525 5.132 5350 Z= 0.283 Chirality : 0.043 0.158 593 Planarity : 0.004 0.040 681 Dihedral : 4.943 56.650 522 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.86 % Allowed : 10.90 % Favored : 87.24 % 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: 1.30 (0.39), residues: 473 helix: 1.57 (0.34), residues: 236 sheet: 0.17 (0.52), residues: 89 loop : 0.34 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1320 HIS 0.002 0.001 HIS A1508 PHE 0.011 0.001 PHE B 90 TYR 0.011 0.001 TYR A1432 ARG 0.005 0.000 ARG B 68 *********************** 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 to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.459 Fit side-chains REVERT: A 1349 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7077 (mp0) REVERT: A 1352 ASN cc_start: 0.8360 (t0) cc_final: 0.7875 (t0) REVERT: A 1398 LEU cc_start: 0.7659 (mt) cc_final: 0.7395 (mm) REVERT: A 1410 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: A 1479 ASN cc_start: 0.7999 (m-40) cc_final: 0.7093 (p0) REVERT: A 1490 GLU cc_start: 0.7138 (tp30) cc_final: 0.6815 (tp30) REVERT: A 1505 ARG cc_start: 0.6960 (mpp80) cc_final: 0.6597 (mtt180) REVERT: A 1507 ARG cc_start: 0.6610 (mmt-90) cc_final: 0.6268 (mmt90) REVERT: B 107 ASN cc_start: 0.7686 (m-40) cc_final: 0.7412 (m-40) REVERT: B 120 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.5383 (ttt-90) REVERT: B 128 LYS cc_start: 0.7864 (mttt) cc_final: 0.7273 (mppt) outliers start: 8 outliers final: 2 residues processed: 83 average time/residue: 1.2537 time to fit residues: 107.6801 Evaluate side-chains 72 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.195826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161685 restraints weight = 4046.287| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.27 r_work: 0.3863 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2276 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= 0.192 Angle : 0.520 6.942 5350 Z= 0.273 Chirality : 0.043 0.175 593 Planarity : 0.004 0.043 681 Dihedral : 4.876 57.045 521 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.25 % Allowed : 10.67 % Favored : 86.08 % 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: 1.36 (0.39), residues: 473 helix: 1.71 (0.34), residues: 236 sheet: 0.24 (0.52), residues: 91 loop : 0.16 (0.54), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 56 HIS 0.002 0.001 HIS A1508 PHE 0.012 0.001 PHE A1518 TYR 0.012 0.001 TYR B 32 ARG 0.002 0.000 ARG A1309 *********************** 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 85 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.446 Fit side-chains REVERT: A 1322 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6518 (ttt) REVERT: A 1349 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7253 (mp0) REVERT: A 1352 ASN cc_start: 0.8234 (t0) cc_final: 0.7791 (t0) REVERT: A 1398 LEU cc_start: 0.7743 (mt) cc_final: 0.7511 (mm) REVERT: A 1410 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: A 1479 ASN cc_start: 0.7969 (m-40) cc_final: 0.7183 (p0) REVERT: A 1490 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: B 107 ASN cc_start: 0.7717 (m-40) cc_final: 0.7464 (m-40) REVERT: B 120 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.5397 (ttt-90) REVERT: B 128 LYS cc_start: 0.7990 (mttt) cc_final: 0.7407 (mppt) REVERT: B 156 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8083 (mm-30) outliers start: 14 outliers final: 3 residues processed: 77 average time/residue: 1.1695 time to fit residues: 93.3083 Evaluate side-chains 71 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.194821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159516 restraints weight = 4021.775| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.29 r_work: 0.3826 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2455 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= 0.175 Angle : 0.502 6.271 5350 Z= 0.263 Chirality : 0.042 0.148 593 Planarity : 0.004 0.045 681 Dihedral : 4.851 56.826 521 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.02 % Allowed : 12.30 % Favored : 84.69 % 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: 1.51 (0.39), residues: 473 helix: 1.87 (0.34), residues: 237 sheet: 0.23 (0.53), residues: 91 loop : 0.21 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1558 HIS 0.002 0.001 HIS A1508 PHE 0.013 0.001 PHE A1518 TYR 0.021 0.001 TYR B 32 ARG 0.003 0.000 ARG A1428 *********************** 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 79 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.453 Fit side-chains REVERT: A 1322 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6582 (ttt) REVERT: A 1349 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7083 (mp0) REVERT: A 1352 ASN cc_start: 0.8139 (t0) cc_final: 0.7723 (t0) REVERT: A 1374 VAL cc_start: 0.7877 (t) cc_final: 0.7649 (t) REVERT: A 1410 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: A 1479 ASN cc_start: 0.7977 (m-40) cc_final: 0.7097 (p0) REVERT: A 1490 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: A 1558 TRP cc_start: 0.7239 (p-90) cc_final: 0.6952 (p-90) REVERT: B 107 ASN cc_start: 0.7665 (m-40) cc_final: 0.7402 (m-40) REVERT: B 120 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.5305 (ttt-90) REVERT: B 128 LYS cc_start: 0.7865 (mttt) cc_final: 0.7288 (mppt) REVERT: B 156 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8125 (mm-30) outliers start: 13 outliers final: 4 residues processed: 73 average time/residue: 1.1228 time to fit residues: 85.0020 Evaluate side-chains 73 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1451 LYS Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.193584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158175 restraints weight = 4120.851| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.32 r_work: 0.3811 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2588 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= 0.194 Angle : 0.526 7.675 5350 Z= 0.271 Chirality : 0.042 0.134 593 Planarity : 0.004 0.047 681 Dihedral : 4.867 55.126 521 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.94 % Allowed : 13.23 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.39), residues: 473 helix: 1.85 (0.34), residues: 237 sheet: 0.19 (0.53), residues: 91 loop : 0.10 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 56 HIS 0.002 0.001 HIS A1508 PHE 0.011 0.001 PHE A1518 TYR 0.010 0.001 TYR A1404 ARG 0.002 0.000 ARG A1528 *********************** 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 82 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.424 Fit side-chains REVERT: A 1322 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6626 (ttt) REVERT: A 1352 ASN cc_start: 0.8150 (t0) cc_final: 0.7708 (t0) REVERT: A 1374 VAL cc_start: 0.7912 (t) cc_final: 0.7684 (t) REVERT: A 1410 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: A 1479 ASN cc_start: 0.8012 (m-40) cc_final: 0.7130 (p0) REVERT: A 1490 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: A 1558 TRP cc_start: 0.7232 (p-90) cc_final: 0.6623 (p-90) REVERT: B 102 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7470 (tpp-160) REVERT: B 107 ASN cc_start: 0.7661 (m-40) cc_final: 0.7413 (m-40) REVERT: B 120 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5415 (ttt-90) REVERT: B 128 LYS cc_start: 0.7904 (mttt) cc_final: 0.7331 (mppt) REVERT: B 156 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8153 (mm-30) outliers start: 17 outliers final: 4 residues processed: 73 average time/residue: 1.1947 time to fit residues: 90.4236 Evaluate side-chains 75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.193985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.158742 restraints weight = 3995.930| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.28 r_work: 0.3810 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2650 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= 0.186 Angle : 0.531 8.439 5350 Z= 0.271 Chirality : 0.042 0.134 593 Planarity : 0.004 0.048 681 Dihedral : 4.833 54.138 521 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.48 % Allowed : 14.62 % Favored : 81.90 % 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 (0.39), residues: 473 helix: 1.95 (0.34), residues: 237 sheet: 0.21 (0.53), residues: 91 loop : 0.11 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 56 HIS 0.002 0.001 HIS A1508 PHE 0.009 0.001 PHE A1518 TYR 0.021 0.001 TYR B 32 ARG 0.002 0.000 ARG A1528 *********************** 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 82 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.514 Fit side-chains REVERT: A 1322 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6609 (ttt) REVERT: A 1349 GLU cc_start: 0.7804 (tm-30) cc_final: 0.6853 (mp0) REVERT: A 1352 ASN cc_start: 0.8098 (t0) cc_final: 0.7652 (t0) REVERT: A 1361 LYS cc_start: 0.6638 (tmtm) cc_final: 0.6301 (ttpp) REVERT: A 1374 VAL cc_start: 0.7869 (t) cc_final: 0.7647 (t) REVERT: A 1395 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 1410 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 1479 ASN cc_start: 0.8026 (m-40) cc_final: 0.7089 (p0) REVERT: A 1490 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: A 1558 TRP cc_start: 0.7156 (p-90) cc_final: 0.6573 (p-90) REVERT: B 102 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7469 (tpp-160) REVERT: B 107 ASN cc_start: 0.7650 (m-40) cc_final: 0.7402 (m-40) REVERT: B 120 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.5467 (ttt-90) REVERT: B 128 LYS cc_start: 0.7883 (mttt) cc_final: 0.7306 (mppt) REVERT: B 156 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8199 (mm-30) outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 1.1776 time to fit residues: 90.2512 Evaluate side-chains 74 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.192366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.156953 restraints weight = 4059.148| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.31 r_work: 0.3796 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2737 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= 0.218 Angle : 0.555 9.497 5350 Z= 0.284 Chirality : 0.043 0.136 593 Planarity : 0.004 0.050 681 Dihedral : 4.916 52.254 521 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.02 % Allowed : 15.78 % Favored : 81.21 % 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: 1.41 (0.39), residues: 473 helix: 1.85 (0.34), residues: 237 sheet: 0.17 (0.53), residues: 91 loop : 0.04 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 56 HIS 0.002 0.001 HIS A1508 PHE 0.009 0.001 PHE A1518 TYR 0.010 0.002 TYR A1404 ARG 0.002 0.000 ARG A1528 *********************** 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 to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.449 Fit side-chains REVERT: A 1322 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6491 (ttt) REVERT: A 1349 GLU cc_start: 0.7782 (tm-30) cc_final: 0.6750 (mp0) REVERT: A 1352 ASN cc_start: 0.8157 (t0) cc_final: 0.7717 (t0) REVERT: A 1361 LYS cc_start: 0.6611 (tmtm) cc_final: 0.6277 (ttpp) REVERT: A 1374 VAL cc_start: 0.7885 (t) cc_final: 0.7659 (t) REVERT: A 1395 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 1410 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 1479 ASN cc_start: 0.8025 (m-40) cc_final: 0.7092 (p0) REVERT: A 1490 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 1558 TRP cc_start: 0.7244 (p-90) cc_final: 0.6621 (p-90) REVERT: B 102 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7515 (tpp-160) REVERT: B 107 ASN cc_start: 0.7677 (m-40) cc_final: 0.7422 (m-40) REVERT: B 120 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.5496 (ttt-90) REVERT: B 128 LYS cc_start: 0.7899 (mttt) cc_final: 0.7313 (mppt) REVERT: B 145 MET cc_start: 0.7159 (tpp) cc_final: 0.6833 (ttt) REVERT: B 156 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8155 (mm-30) outliers start: 13 outliers final: 5 residues processed: 71 average time/residue: 1.1337 time to fit residues: 83.4041 Evaluate side-chains 74 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158303 restraints weight = 4018.420| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.29 r_work: 0.3818 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2762 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= 0.190 Angle : 0.543 10.961 5350 Z= 0.277 Chirality : 0.042 0.133 593 Planarity : 0.004 0.051 681 Dihedral : 4.873 51.751 521 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.48 % Allowed : 15.78 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.39), residues: 473 helix: 1.94 (0.34), residues: 237 sheet: 0.19 (0.54), residues: 91 loop : 0.09 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 56 HIS 0.002 0.001 HIS A1585 PHE 0.009 0.001 PHE A1518 TYR 0.024 0.002 TYR B 32 ARG 0.002 0.000 ARG A1528 *********************** 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 81 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.457 Fit side-chains REVERT: A 1322 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6473 (ttt) REVERT: A 1349 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6749 (mp0) REVERT: A 1352 ASN cc_start: 0.8122 (t0) cc_final: 0.7708 (t0) REVERT: A 1361 LYS cc_start: 0.6660 (tmtm) cc_final: 0.6315 (ttpp) REVERT: A 1374 VAL cc_start: 0.7901 (t) cc_final: 0.7675 (t) REVERT: A 1395 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 1399 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6734 (tt0) REVERT: A 1410 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 1479 ASN cc_start: 0.8039 (m-40) cc_final: 0.7083 (p0) REVERT: A 1490 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: A 1558 TRP cc_start: 0.7247 (p-90) cc_final: 0.6618 (p-90) REVERT: B 102 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7460 (tpp-160) REVERT: B 107 ASN cc_start: 0.7705 (m-40) cc_final: 0.7451 (m-40) REVERT: B 120 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5547 (ttt-90) REVERT: B 128 LYS cc_start: 0.7899 (mttt) cc_final: 0.7316 (mppt) REVERT: B 145 MET cc_start: 0.7083 (tpp) cc_final: 0.6791 (ttt) REVERT: B 156 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8158 (mm-30) outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 1.2276 time to fit residues: 92.8001 Evaluate side-chains 75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1410 GLN Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.190703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155411 restraints weight = 4031.262| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.29 r_work: 0.3786 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3964 Z= 0.268 Angle : 0.594 11.499 5350 Z= 0.305 Chirality : 0.044 0.140 593 Planarity : 0.005 0.050 681 Dihedral : 5.039 49.378 521 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.94 % Allowed : 15.55 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.39), residues: 473 helix: 1.73 (0.34), residues: 235 sheet: 0.12 (0.54), residues: 91 loop : -0.11 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 56 HIS 0.003 0.001 HIS A1351 PHE 0.009 0.001 PHE A1555 TYR 0.012 0.002 TYR A1404 ARG 0.003 0.000 ARG A1309 *********************** 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 81 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.415 Fit side-chains REVERT: A 1322 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6393 (ttt) REVERT: A 1352 ASN cc_start: 0.8228 (t0) cc_final: 0.7837 (t0) REVERT: A 1395 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 1399 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6756 (tt0) REVERT: A 1479 ASN cc_start: 0.8026 (m-40) cc_final: 0.7062 (p0) REVERT: A 1490 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7077 (tp30) REVERT: A 1558 TRP cc_start: 0.7321 (p-90) cc_final: 0.6614 (p-90) REVERT: B 102 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7521 (tpp-160) REVERT: B 107 ASN cc_start: 0.7772 (m-40) cc_final: 0.7527 (m-40) REVERT: B 120 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.5663 (ttt-90) REVERT: B 128 LYS cc_start: 0.7964 (mttt) cc_final: 0.7377 (mppt) REVERT: B 133 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6620 (mptp) outliers start: 17 outliers final: 8 residues processed: 72 average time/residue: 1.1634 time to fit residues: 86.7021 Evaluate side-chains 75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.194495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.159394 restraints weight = 4066.227| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.30 r_work: 0.3821 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3964 Z= 0.195 Angle : 0.581 12.087 5350 Z= 0.297 Chirality : 0.041 0.131 593 Planarity : 0.004 0.048 681 Dihedral : 4.879 49.531 521 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.25 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 473 helix: 1.91 (0.34), residues: 236 sheet: 0.17 (0.55), residues: 91 loop : -0.11 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 56 HIS 0.002 0.001 HIS A1585 PHE 0.009 0.001 PHE A1518 TYR 0.025 0.001 TYR B 32 ARG 0.003 0.000 ARG A1309 ********************** 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 80 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.422 Fit side-chains REVERT: A 1322 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6504 (ttt) REVERT: A 1349 GLU cc_start: 0.7779 (tm-30) cc_final: 0.6817 (mp0) REVERT: A 1352 ASN cc_start: 0.8109 (t0) cc_final: 0.7727 (t0) REVERT: A 1374 VAL cc_start: 0.7913 (t) cc_final: 0.7686 (t) REVERT: A 1395 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 1399 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6771 (tt0) REVERT: A 1479 ASN cc_start: 0.8027 (m-40) cc_final: 0.7069 (p0) REVERT: A 1490 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: A 1558 TRP cc_start: 0.7288 (p-90) cc_final: 0.6586 (p-90) REVERT: B 102 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7457 (tpp-160) REVERT: B 107 ASN cc_start: 0.7788 (m-40) cc_final: 0.7533 (m-40) REVERT: B 120 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5545 (ttt-90) REVERT: B 128 LYS cc_start: 0.7942 (mttt) cc_final: 0.7356 (mppt) REVERT: B 133 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6625 (mptp) REVERT: B 156 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 14 outliers final: 7 residues processed: 72 average time/residue: 1.1184 time to fit residues: 83.4953 Evaluate side-chains 74 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain A residue 1490 GLU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.197148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162129 restraints weight = 3974.558| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.29 r_work: 0.3857 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3048 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= 0.178 Angle : 0.566 11.827 5350 Z= 0.289 Chirality : 0.040 0.131 593 Planarity : 0.004 0.047 681 Dihedral : 4.753 48.800 521 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.32 % Allowed : 17.40 % Favored : 80.28 % 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: 1.49 (0.39), residues: 473 helix: 2.03 (0.34), residues: 236 sheet: 0.15 (0.55), residues: 91 loop : -0.10 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 56 HIS 0.001 0.000 HIS B 104 PHE 0.009 0.001 PHE A1518 TYR 0.011 0.001 TYR A1533 ARG 0.003 0.000 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3507.64 seconds wall clock time: 60 minutes 37.31 seconds (3637.31 seconds total)