Starting phenix.real_space_refine on Mon Mar 11 01:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9v_37382/03_2024/8w9v_37382.pdb" } resolution = 2.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 46 5.16 5 C 4324 2.51 5 N 1054 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 98": "OE1" <-> "OE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3284 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.17, per 1000 atoms: 0.63 Number of scatterers: 6574 At special positions: 0 Unit cell: (102.3, 86.49, 87.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 46 16.00 O 1144 8.00 N 1054 7.00 C 4324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 42 through 65 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.509A pdb=" N MET A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 179 through 216 Processing helix chain 'A' and resid 216 through 227 Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.712A pdb=" N SER A 258 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 277 through 293 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.758A pdb=" N ASP A 348 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.739A pdb=" N ARG A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'B' and resid 42 through 65 Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.502A pdb=" N MET B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 179 through 216 removed outlier: 3.527A pdb=" N HIS B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.713A pdb=" N SER B 258 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.519A pdb=" N GLN B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.582A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 315 through 341 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.775A pdb=" N ASP B 348 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.540A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 393 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 479 through 485 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'B' and resid 520 through 525 449 hydrogen bonds defined for protein. 1317 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: 1.73 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1036 1.32 - 1.45: 1764 1.45 - 1.57: 3844 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6718 Sorted by residual: bond pdb=" C ASN A 253 " pdb=" O ASN A 253 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.26e-02 6.30e+03 7.28e+00 bond pdb=" C ASN B 253 " pdb=" O ASN B 253 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.26e-02 6.30e+03 3.58e+00 bond pdb=" CB PRO B 430 " pdb=" CG PRO B 430 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.16e+00 bond pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.22e-02 6.72e+03 1.41e+00 bond pdb=" CA ASN A 253 " pdb=" C ASN A 253 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.34e-02 5.57e+03 1.30e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.43: 195 106.43 - 113.31: 3804 113.31 - 120.19: 2285 120.19 - 127.07: 2776 127.07 - 133.95: 74 Bond angle restraints: 9134 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" CD PRO B 430 " ideal model delta sigma weight residual 112.00 108.11 3.89 1.40e+00 5.10e-01 7.70e+00 angle pdb=" C THR B 88 " pdb=" N VAL B 89 " pdb=" CA VAL B 89 " ideal model delta sigma weight residual 121.97 126.41 -4.44 1.80e+00 3.09e-01 6.07e+00 angle pdb=" O THR A 88 " pdb=" C THR A 88 " pdb=" N VAL A 89 " ideal model delta sigma weight residual 122.42 126.18 -3.76 1.61e+00 3.86e-01 5.45e+00 angle pdb=" C THR A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.23e+00 ... (remaining 9129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 3400 13.84 - 27.68: 390 27.68 - 41.52: 107 41.52 - 55.36: 57 55.36 - 69.20: 4 Dihedral angle restraints: 3958 sinusoidal: 1500 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ASN B 365 " pdb=" C ASN B 365 " pdb=" N ALA B 366 " pdb=" CA ALA B 366 " ideal model delta harmonic sigma weight residual 180.00 163.57 16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ASN B 275 " pdb=" CB ASN B 275 " pdb=" CG ASN B 275 " pdb=" OD1 ASN B 275 " ideal model delta sinusoidal sigma weight residual -90.00 -159.20 69.20 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN A 365 " pdb=" C ASN A 365 " pdb=" N ALA A 366 " pdb=" CA ALA A 366 " ideal model delta harmonic sigma weight residual 180.00 164.64 15.36 0 5.00e+00 4.00e-02 9.43e+00 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 945 0.052 - 0.104: 147 0.104 - 0.156: 16 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASN B 253 " pdb=" N ASN B 253 " pdb=" C ASN B 253 " pdb=" CB ASN B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 374 " pdb=" N ILE B 374 " pdb=" C ILE B 374 " pdb=" CB ILE B 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1107 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 429 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO B 430 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C GLU A 252 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU A 252 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 253 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 252 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C GLU B 252 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU B 252 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 253 " 0.009 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 1912 2.81 - 3.39: 7634 3.39 - 3.98: 13246 3.98 - 4.56: 19207 4.56 - 5.14: 26759 Nonbonded interactions: 68758 Sorted by model distance: nonbonded pdb=" OE1 GLN B 424 " pdb=" OG SER B 526 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLN A 424 " pdb=" OG SER A 526 " model vdw 2.236 2.440 nonbonded pdb=" O PRO A 430 " pdb=" ND2 ASN A 434 " model vdw 2.245 2.520 nonbonded pdb=" O PHE A 361 " pdb=" ND2 ASN A 365 " model vdw 2.268 2.520 nonbonded pdb=" OH TYR B 197 " pdb=" O ALA B 273 " model vdw 2.272 2.440 ... (remaining 68753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.710 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: 2.450 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.210 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.074 6718 Z= 0.197 Angle : 0.480 6.581 9134 Z= 0.253 Chirality : 0.038 0.260 1110 Planarity : 0.004 0.070 1108 Dihedral : 14.065 69.196 2370 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.93 % Allowed : 15.07 % Favored : 84.00 % 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: 1.62 (0.28), residues: 840 helix: 1.69 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 45 HIS 0.004 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.016 0.002 TYR A 50 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.796 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 1.1046 time to fit residues: 101.9416 Evaluate side-chains 84 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 457 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 270 GLN B 253 ASN B 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6718 Z= 0.221 Angle : 0.485 5.720 9134 Z= 0.250 Chirality : 0.038 0.117 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.862 54.849 904 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.33 % Allowed : 12.93 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.28), residues: 840 helix: 2.10 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.57 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 45 HIS 0.005 0.001 HIS B 368 PHE 0.012 0.001 PHE A 198 TYR 0.015 0.002 TYR A 50 ARG 0.002 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 0.794 Fit side-chains REVERT: A 354 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: B 185 ARG cc_start: 0.6946 (mtt90) cc_final: 0.6280 (mmm-85) REVERT: B 299 ARG cc_start: 0.7399 (mtm180) cc_final: 0.6917 (mtm180) outliers start: 25 outliers final: 14 residues processed: 91 average time/residue: 1.1080 time to fit residues: 106.9459 Evaluate side-chains 95 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN B 368 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6718 Z= 0.151 Angle : 0.443 5.137 9134 Z= 0.227 Chirality : 0.036 0.114 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.140 46.620 898 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.80 % Allowed : 14.13 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.28), residues: 840 helix: 2.40 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.004 0.001 HIS B 368 PHE 0.011 0.001 PHE A 198 TYR 0.014 0.002 TYR A 50 ARG 0.004 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.745 Fit side-chains REVERT: B 185 ARG cc_start: 0.6972 (mtt90) cc_final: 0.6307 (mmm-85) REVERT: B 299 ARG cc_start: 0.7390 (mtm180) cc_final: 0.6943 (mtm180) REVERT: B 450 ARG cc_start: 0.7626 (ttm170) cc_final: 0.6909 (ttp-110) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 1.0708 time to fit residues: 101.6846 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 461 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0050 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6718 Z= 0.151 Angle : 0.437 5.394 9134 Z= 0.224 Chirality : 0.036 0.112 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.125 46.941 898 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.47 % Allowed : 14.00 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.28), residues: 840 helix: 2.50 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.004 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.015 0.002 TYR A 50 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 0.780 Fit side-chains REVERT: B 185 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6288 (mmm-85) REVERT: B 299 ARG cc_start: 0.7350 (mtm180) cc_final: 0.6910 (mtm180) REVERT: B 461 MET cc_start: 0.9008 (mmm) cc_final: 0.8769 (OUTLIER) outliers start: 26 outliers final: 16 residues processed: 91 average time/residue: 1.0273 time to fit residues: 99.5819 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6718 Z= 0.205 Angle : 0.463 5.831 9134 Z= 0.237 Chirality : 0.038 0.117 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.266 49.016 898 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.60 % Allowed : 14.00 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.28), residues: 840 helix: 2.42 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS B 368 PHE 0.012 0.001 PHE A 198 TYR 0.015 0.002 TYR A 50 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 0.903 Fit side-chains REVERT: B 185 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6347 (mmm-85) REVERT: B 299 ARG cc_start: 0.7326 (mtm180) cc_final: 0.6892 (mtm180) outliers start: 27 outliers final: 18 residues processed: 90 average time/residue: 1.1127 time to fit residues: 107.0640 Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 368 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6718 Z= 0.142 Angle : 0.441 8.605 9134 Z= 0.225 Chirality : 0.036 0.112 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.173 48.956 898 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.93 % Allowed : 15.20 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.28), residues: 840 helix: 2.61 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.004 0.001 HIS A 368 PHE 0.011 0.001 PHE A 198 TYR 0.013 0.001 TYR A 50 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.400 Fit side-chains REVERT: A 292 LEU cc_start: 0.8024 (mp) cc_final: 0.7813 (tt) REVERT: A 299 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7059 (mtm180) REVERT: B 57 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 185 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6385 (mmm-85) REVERT: B 299 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6893 (mtm180) outliers start: 22 outliers final: 15 residues processed: 88 average time/residue: 1.1848 time to fit residues: 111.8295 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6718 Z= 0.236 Angle : 0.476 6.254 9134 Z= 0.245 Chirality : 0.038 0.120 1110 Planarity : 0.004 0.049 1108 Dihedral : 4.385 50.982 898 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.33 % Allowed : 14.93 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.28), residues: 840 helix: 2.44 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.005 0.001 HIS B 368 PHE 0.013 0.001 PHE A 198 TYR 0.015 0.002 TYR A 50 ARG 0.001 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.796 Fit side-chains REVERT: A 299 ARG cc_start: 0.7466 (mtm180) cc_final: 0.7082 (mtm180) REVERT: B 185 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6381 (mmm-85) REVERT: B 299 ARG cc_start: 0.7334 (mtm180) cc_final: 0.6899 (mtm180) outliers start: 25 outliers final: 18 residues processed: 89 average time/residue: 1.0040 time to fit residues: 95.3381 Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 0.0020 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6718 Z= 0.176 Angle : 0.451 5.064 9134 Z= 0.234 Chirality : 0.037 0.114 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.333 51.600 898 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.93 % Allowed : 15.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.28), residues: 840 helix: 2.54 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 503 HIS 0.004 0.001 HIS B 368 PHE 0.012 0.001 PHE A 198 TYR 0.013 0.002 TYR B 50 ARG 0.001 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.794 Fit side-chains REVERT: A 292 LEU cc_start: 0.8026 (mp) cc_final: 0.7792 (tt) REVERT: A 299 ARG cc_start: 0.7436 (mtm180) cc_final: 0.7052 (mtm180) REVERT: A 306 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 532 LYS cc_start: 0.7546 (mmtm) cc_final: 0.7043 (mmtp) REVERT: B 185 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6330 (mmm-85) REVERT: B 299 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6870 (mtm180) outliers start: 22 outliers final: 17 residues processed: 88 average time/residue: 1.0465 time to fit residues: 98.0971 Evaluate side-chains 98 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6718 Z= 0.129 Angle : 0.437 7.043 9134 Z= 0.225 Chirality : 0.036 0.112 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.181 50.793 898 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.53 % Allowed : 16.00 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.28), residues: 840 helix: 2.70 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.50 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 287 HIS 0.003 0.000 HIS B 368 PHE 0.010 0.001 PHE A 198 TYR 0.012 0.001 TYR B 50 ARG 0.001 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.796 Fit side-chains REVERT: A 299 ARG cc_start: 0.7441 (mtm180) cc_final: 0.7059 (mtm180) REVERT: A 301 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7914 (ttm) REVERT: A 306 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 532 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7041 (mmtp) REVERT: B 185 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6288 (mmm-85) REVERT: B 299 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6812 (mtm180) REVERT: B 450 ARG cc_start: 0.7640 (ttm170) cc_final: 0.6931 (ttp-110) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 1.1178 time to fit residues: 102.0703 Evaluate side-chains 95 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 368 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6718 Z= 0.185 Angle : 0.474 8.162 9134 Z= 0.239 Chirality : 0.037 0.113 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.280 51.313 898 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.93 % Allowed : 15.73 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.28), residues: 840 helix: 2.59 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 502 HIS 0.004 0.001 HIS B 368 PHE 0.012 0.001 PHE A 198 TYR 0.014 0.002 TYR B 50 ARG 0.001 0.000 ARG A 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.828 Fit side-chains REVERT: A 299 ARG cc_start: 0.7439 (mtm180) cc_final: 0.7080 (mtm180) REVERT: A 306 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 532 LYS cc_start: 0.7545 (mmtm) cc_final: 0.7043 (mmtp) REVERT: B 185 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6316 (mmm-85) REVERT: B 299 ARG cc_start: 0.7272 (mtm180) cc_final: 0.6822 (mtm180) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 1.0777 time to fit residues: 100.8710 Evaluate side-chains 97 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 0.0000 chunk 48 optimal weight: 3.9990 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.094601 restraints weight = 8197.500| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.35 r_work: 0.2910 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.120 Angle : 0.433 6.946 9134 Z= 0.223 Chirality : 0.036 0.113 1110 Planarity : 0.004 0.048 1108 Dihedral : 4.113 50.091 898 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.27 % Allowed : 16.67 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.28), residues: 840 helix: 2.76 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 531 HIS 0.002 0.001 HIS A 368 PHE 0.010 0.001 PHE A 198 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.62 seconds wall clock time: 42 minutes 55.38 seconds (2575.38 seconds total)