Starting phenix.real_space_refine on Mon Jun 24 15:06:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgr_50418/06_2024/9fgr_50418.pdb" } resolution = 4.0 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= -0.003 sd= 0.051 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 14 5.16 5 C 2042 2.51 5 N 537 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3209 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1511 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1683 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.61, per 1000 atoms: 1.12 Number of scatterers: 3209 At special positions: 0 Unit cell: (82.677, 62.23, 81.788, 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 14 16.00 O 616 8.00 N 537 7.00 C 2042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 753.3 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.3% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.099A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.389A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.963A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.015A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.959A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 22 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY E 10 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR E 115 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 50 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 58 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.514A pdb=" N THR E 138 " --> pdb=" O ARG E 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 188 removed outlier: 5.792A pdb=" N LEU E 180 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN E 171 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 182 " --> pdb=" O TRP E 169 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1025 1.35 - 1.47: 884 1.47 - 1.59: 1362 1.59 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3287 Sorted by residual: bond pdb=" CA THR C 470 " pdb=" CB THR C 470 " ideal model delta sigma weight residual 1.528 1.583 -0.055 2.61e-02 1.47e+03 4.40e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C3 NAG C1301 " pdb=" O3 NAG C1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.80e-01 bond pdb=" C2 NAG C1301 " pdb=" N2 NAG C1301 " ideal model delta sigma weight residual 1.439 1.457 -0.018 2.00e-02 2.50e+03 7.88e-01 ... (remaining 3282 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 87 107.14 - 113.84: 1720 113.84 - 120.55: 1249 120.55 - 127.25: 1377 127.25 - 133.96: 30 Bond angle restraints: 4463 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.03 -6.22 2.21e+00 2.05e-01 7.92e+00 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 112.37 -3.77 1.46e+00 4.69e-01 6.67e+00 angle pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " pdb=" CG LYS C 386 " ideal model delta sigma weight residual 114.10 118.22 -4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" N GLY E 198 " pdb=" CA GLY E 198 " pdb=" C GLY E 198 " ideal model delta sigma weight residual 110.90 114.03 -3.13 1.53e+00 4.27e-01 4.18e+00 angle pdb=" N SER E 35 " pdb=" CA SER E 35 " pdb=" C SER E 35 " ideal model delta sigma weight residual 108.55 111.69 -3.14 1.62e+00 3.81e-01 3.75e+00 ... (remaining 4458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 1748 16.77 - 33.55: 154 33.55 - 50.32: 37 50.32 - 67.09: 3 67.09 - 83.87: 1 Dihedral angle restraints: 1943 sinusoidal: 764 harmonic: 1179 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 142.95 -49.95 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual -86.00 -128.20 42.20 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.80 -23.20 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 1940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 327 0.034 - 0.069: 100 0.069 - 0.103: 37 0.103 - 0.137: 16 0.137 - 0.171: 1 Chirality restraints: 481 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA SER E 228 " pdb=" N SER E 228 " pdb=" C SER E 228 " pdb=" CB SER E 228 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 182 " pdb=" N ILE E 182 " pdb=" C ILE E 182 " pdb=" CB ILE E 182 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 478 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 147 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 148 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 140 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO E 141 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 141 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 141 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 499 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.017 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 126 2.72 - 3.27: 3136 3.27 - 3.81: 4692 3.81 - 4.36: 5568 4.36 - 4.90: 9744 Nonbonded interactions: 23266 Sorted by model distance: nonbonded pdb=" OG SER E 147 " pdb=" OE1 GLU E 150 " model vdw 2.176 2.440 nonbonded pdb=" O ALA C 475 " pdb=" OG1 THR E 28 " model vdw 2.186 2.440 nonbonded pdb=" OG SER E 159 " pdb=" OE1 GLN E 160 " model vdw 2.206 2.440 nonbonded pdb=" O ALA E 104 " pdb=" OH TYR E 170 " model vdw 2.212 2.440 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.286 2.440 ... (remaining 23261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.840 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.003 0.055 3287 Z= 0.171 Angle : 0.576 6.219 4463 Z= 0.308 Chirality : 0.042 0.171 481 Planarity : 0.004 0.036 578 Dihedral : 12.554 83.866 1181 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 404 helix: -4.11 (0.47), residues: 20 sheet: 0.12 (0.52), residues: 112 loop : -1.33 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 169 PHE 0.014 0.001 PHE C 429 TYR 0.011 0.001 TYR E 225 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (m-30) REVERT: E 238 ARG cc_start: 0.7467 (pmt170) cc_final: 0.6991 (ptp90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1644 time to fit residues: 15.2074 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3287 Z= 0.154 Angle : 0.559 5.962 4463 Z= 0.289 Chirality : 0.042 0.152 481 Planarity : 0.004 0.035 578 Dihedral : 5.366 53.695 476 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.03 % Allowed : 11.01 % Favored : 86.96 % 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: -1.28 (0.40), residues: 404 helix: -3.85 (0.57), residues: 23 sheet: 0.41 (0.48), residues: 120 loop : -1.23 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 PHE 0.016 0.001 PHE E 205 TYR 0.016 0.001 TYR C 473 ARG 0.001 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.358 Fit side-chains REVERT: C 357 ARG cc_start: 0.7646 (mtp85) cc_final: 0.6401 (mtm180) REVERT: E 238 ARG cc_start: 0.7020 (pmt170) cc_final: 0.6673 (ptp90) outliers start: 7 outliers final: 3 residues processed: 73 average time/residue: 0.1531 time to fit residues: 13.5935 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 36 optimal weight: 0.0060 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3287 Z= 0.231 Angle : 0.572 6.099 4463 Z= 0.299 Chirality : 0.042 0.146 481 Planarity : 0.004 0.036 578 Dihedral : 5.594 54.218 476 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.19 % Allowed : 13.33 % Favored : 83.48 % 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: -1.37 (0.40), residues: 404 helix: -3.81 (0.58), residues: 23 sheet: 0.35 (0.47), residues: 126 loop : -1.35 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.015 0.002 PHE E 205 TYR 0.012 0.001 TYR C 453 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.320 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.1596 time to fit residues: 13.7740 Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3287 Z= 0.206 Angle : 0.571 6.254 4463 Z= 0.295 Chirality : 0.043 0.150 481 Planarity : 0.004 0.036 578 Dihedral : 5.596 54.441 476 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.77 % Allowed : 14.20 % Favored : 82.03 % 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: -1.38 (0.40), residues: 404 helix: -3.69 (0.66), residues: 23 sheet: 0.39 (0.47), residues: 127 loop : -1.40 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.011 0.001 PHE E 205 TYR 0.017 0.001 TYR C 473 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.302 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.1567 time to fit residues: 13.4865 Evaluate side-chains 64 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 7 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3287 Z= 0.190 Angle : 0.569 6.282 4463 Z= 0.292 Chirality : 0.043 0.149 481 Planarity : 0.004 0.034 578 Dihedral : 5.499 54.187 476 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.48 % Allowed : 16.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.40), residues: 404 helix: -3.66 (0.68), residues: 23 sheet: 0.62 (0.49), residues: 122 loop : -1.41 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.011 0.001 PHE E 155 TYR 0.009 0.001 TYR C 453 ARG 0.001 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.387 Fit side-chains REVERT: E 238 ARG cc_start: 0.7468 (pmt170) cc_final: 0.7091 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.1493 time to fit residues: 12.7048 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3287 Z= 0.206 Angle : 0.578 6.187 4463 Z= 0.299 Chirality : 0.043 0.139 481 Planarity : 0.004 0.034 578 Dihedral : 5.536 54.287 476 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.48 % Allowed : 17.10 % Favored : 79.42 % 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 (0.40), residues: 404 helix: -3.63 (0.68), residues: 23 sheet: 0.54 (0.48), residues: 127 loop : -1.35 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.010 0.001 PHE E 205 TYR 0.022 0.001 TYR C 473 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.374 Fit side-chains REVERT: E 238 ARG cc_start: 0.7602 (pmt170) cc_final: 0.7129 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1518 time to fit residues: 12.3463 Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3287 Z= 0.197 Angle : 0.583 6.130 4463 Z= 0.301 Chirality : 0.042 0.138 481 Planarity : 0.004 0.034 578 Dihedral : 5.518 54.243 476 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 17.97 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.41), residues: 404 helix: -3.59 (0.69), residues: 23 sheet: 0.73 (0.49), residues: 122 loop : -1.34 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.008 0.001 PHE E 205 TYR 0.009 0.001 TYR E 52 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.359 Fit side-chains REVERT: C 378 LYS cc_start: 0.8468 (mttp) cc_final: 0.7840 (mmtm) REVERT: E 238 ARG cc_start: 0.7577 (pmt170) cc_final: 0.7142 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.1465 time to fit residues: 11.7950 Evaluate side-chains 61 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.0010 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3287 Z= 0.171 Angle : 0.574 6.666 4463 Z= 0.295 Chirality : 0.042 0.136 481 Planarity : 0.004 0.034 578 Dihedral : 5.388 54.007 476 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.48 % Allowed : 18.55 % Favored : 77.97 % 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: -1.12 (0.41), residues: 404 helix: -3.51 (0.73), residues: 23 sheet: 0.76 (0.50), residues: 122 loop : -1.30 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.018 0.001 PHE E 205 TYR 0.009 0.001 TYR E 52 ARG 0.001 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.372 Fit side-chains REVERT: C 338 PHE cc_start: 0.6822 (p90) cc_final: 0.6556 (p90) REVERT: C 378 LYS cc_start: 0.8443 (mttp) cc_final: 0.7815 (mmtm) REVERT: E 238 ARG cc_start: 0.7472 (pmt170) cc_final: 0.7079 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.1560 time to fit residues: 12.3788 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3287 Z= 0.193 Angle : 0.577 6.392 4463 Z= 0.298 Chirality : 0.042 0.137 481 Planarity : 0.004 0.034 578 Dihedral : 5.444 54.257 476 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.90 % Allowed : 18.84 % Favored : 78.26 % 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: -1.12 (0.41), residues: 404 helix: -3.51 (0.73), residues: 23 sheet: 0.80 (0.50), residues: 122 loop : -1.32 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.016 0.001 PHE E 205 TYR 0.024 0.001 TYR C 473 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.385 Fit side-chains REVERT: C 378 LYS cc_start: 0.8459 (mttp) cc_final: 0.7833 (mmtm) REVERT: E 169 TRP cc_start: 0.8866 (m100) cc_final: 0.8537 (m100) REVERT: E 238 ARG cc_start: 0.7498 (pmt170) cc_final: 0.7086 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 65 average time/residue: 0.1535 time to fit residues: 12.2225 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3287 Z= 0.177 Angle : 0.590 10.970 4463 Z= 0.296 Chirality : 0.042 0.134 481 Planarity : 0.004 0.034 578 Dihedral : 5.375 54.178 476 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.19 % Allowed : 19.13 % Favored : 77.68 % 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: -1.08 (0.41), residues: 404 helix: -3.46 (0.75), residues: 23 sheet: 0.83 (0.50), residues: 122 loop : -1.30 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 PHE 0.015 0.001 PHE E 205 TYR 0.011 0.001 TYR E 170 ARG 0.001 0.000 ARG C 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.359 Fit side-chains REVERT: C 378 LYS cc_start: 0.8432 (mttp) cc_final: 0.7803 (mmtm) REVERT: E 167 LEU cc_start: 0.9110 (tt) cc_final: 0.8703 (tt) REVERT: E 169 TRP cc_start: 0.8836 (m100) cc_final: 0.8543 (m100) REVERT: E 238 ARG cc_start: 0.7430 (pmt170) cc_final: 0.7134 (mtm-85) outliers start: 11 outliers final: 11 residues processed: 69 average time/residue: 0.1508 time to fit residues: 12.7134 Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111611 restraints weight = 6135.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113336 restraints weight = 4690.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114578 restraints weight = 3849.905| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3287 Z= 0.201 Angle : 0.608 11.121 4463 Z= 0.307 Chirality : 0.042 0.136 481 Planarity : 0.004 0.034 578 Dihedral : 5.464 54.122 476 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.77 % Allowed : 18.84 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.41), residues: 404 helix: -3.64 (0.68), residues: 23 sheet: 0.72 (0.49), residues: 128 loop : -1.36 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 PHE 0.013 0.001 PHE C 338 TYR 0.013 0.001 TYR E 52 ARG 0.002 0.000 ARG E 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1289.51 seconds wall clock time: 23 minutes 51.19 seconds (1431.19 seconds total)