Starting phenix.real_space_refine on Thu Nov 14 06:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/11_2024/8ont_17000_trim.cif" } resolution = 3.66 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= 0.063 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 P 1 5.49 5 S 26 5.16 5 C 2831 2.51 5 N 696 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.77 Number of scatterers: 4316 At special positions: 0 Unit cell: (75.516, 96.348, 78.12, 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) S 26 16.00 P 1 15.00 O 762 8.00 N 696 7.00 C 2831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 692.5 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 72.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.546A pdb=" N VAL A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.553A pdb=" N LEU A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 157 Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 159 through 181 removed outlier: 4.672A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 3.684A pdb=" N GLU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 242 through 253 removed outlier: 4.282A pdb=" N PHE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 252 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 300 Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.916A pdb=" N ASP A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.850A pdb=" N LEU A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 325 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 362 removed outlier: 4.042A pdb=" N VAL A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 390 Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 391 through 423 Proline residue: A 411 - end of helix Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 433 through 466 removed outlier: 3.891A pdb=" N HIS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 496 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.693A pdb=" N ARG B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.398A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 939 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: 1.25 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 658 1.31 - 1.43: 1199 1.43 - 1.56: 2509 1.56 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4410 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " ideal model delta sigma weight residual 1.503 1.569 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " ideal model delta sigma weight residual 1.634 1.689 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CB PLC A 601 " pdb=" C1B PLC A 601 " ideal model delta sigma weight residual 1.504 1.556 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 4405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 5947 3.19 - 6.39: 44 6.39 - 9.58: 3 9.58 - 12.77: 1 12.77 - 15.96: 1 Bond angle restraints: 5996 Sorted by residual: angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.58 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 109.11 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C1' PLC A 601 " pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 111.19 119.79 -8.60 3.00e+00 1.11e-01 8.22e+00 angle pdb=" C1B PLC A 601 " pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 111.34 119.59 -8.25 3.00e+00 1.11e-01 7.57e+00 angle pdb=" C ALA A 300 " pdb=" CA ALA A 300 " pdb=" CB ALA A 300 " ideal model delta sigma weight residual 110.42 115.43 -5.01 1.99e+00 2.53e-01 6.34e+00 ... (remaining 5991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.83: 2315 20.83 - 41.66: 234 41.66 - 62.48: 34 62.48 - 83.31: 5 83.31 - 104.14: 6 Dihedral angle restraints: 2594 sinusoidal: 986 harmonic: 1608 Sorted by residual: dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 48.43 -104.14 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C3 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual 67.16 168.71 -101.55 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C2' PLC A 601 " pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sinusoidal sigma weight residual 169.53 79.09 90.44 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 576 0.046 - 0.093: 114 0.093 - 0.139: 20 0.139 - 0.185: 0 0.185 - 0.231: 1 Chirality restraints: 711 Sorted by residual: chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.54 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO A 143 " pdb=" N PRO A 143 " pdb=" C PRO A 143 " pdb=" CB PRO A 143 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 708 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.307 9.50e-02 1.11e+02 1.38e-01 1.17e+01 pdb=" NE ARG B 19 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 87 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 88 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 142 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 143 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.019 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 30 2.51 - 3.10: 3511 3.10 - 3.70: 6575 3.70 - 4.30: 8905 4.30 - 4.90: 15773 Nonbonded interactions: 34794 Sorted by model distance: nonbonded pdb=" OH TYR A 82 " pdb=" OG1 THR A 296 " model vdw 1.908 3.040 nonbonded pdb=" O SER A 139 " pdb=" OG SER A 402 " model vdw 2.025 3.040 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 495 " model vdw 2.071 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" OG1 THR A 346 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR A 351 " pdb=" ND2 ASN A 372 " model vdw 2.083 3.120 ... (remaining 34789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.006 0.107 4410 Z= 0.376 Angle : 0.671 15.964 5996 Z= 0.314 Chirality : 0.038 0.231 711 Planarity : 0.006 0.138 733 Dihedral : 16.916 104.141 1554 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.87 % Allowed : 25.22 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.38), residues: 552 helix: 2.54 (0.27), residues: 360 sheet: -0.03 (0.82), residues: 47 loop : -2.54 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.003 0.001 HIS A 248 PHE 0.014 0.001 PHE A 236 TYR 0.017 0.002 TYR B 80 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.494 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2488 time to fit residues: 16.3065 Evaluate side-chains 54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 372 ASN A 451 ASN A 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4410 Z= 0.295 Angle : 0.609 5.965 5996 Z= 0.311 Chirality : 0.041 0.143 711 Planarity : 0.005 0.039 733 Dihedral : 8.595 79.803 640 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.48 % Allowed : 21.96 % Favored : 74.57 % 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: 1.74 (0.37), residues: 552 helix: 2.60 (0.26), residues: 365 sheet: -0.05 (0.79), residues: 49 loop : -2.62 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.012 0.001 PHE A 236 TYR 0.014 0.001 TYR A 459 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.471 Fit side-chains REVERT: A 248 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6002 (m-70) REVERT: A 371 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6825 (tpt170) REVERT: B 108 SER cc_start: 0.8703 (m) cc_final: 0.8458 (m) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.1975 time to fit residues: 16.5697 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4410 Z= 0.251 Angle : 0.553 6.302 5996 Z= 0.284 Chirality : 0.039 0.136 711 Planarity : 0.005 0.053 733 Dihedral : 8.177 69.407 640 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.91 % Allowed : 21.52 % Favored : 74.57 % 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: 1.92 (0.37), residues: 552 helix: 2.62 (0.26), residues: 363 sheet: 0.30 (0.79), residues: 47 loop : -2.18 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.001 0.001 HIS A 248 PHE 0.009 0.001 PHE A 361 TYR 0.012 0.001 TYR A 459 ARG 0.005 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.464 Fit side-chains REVERT: A 339 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7806 (tt) REVERT: B 108 SER cc_start: 0.8687 (m) cc_final: 0.8429 (m) outliers start: 18 outliers final: 9 residues processed: 65 average time/residue: 0.2213 time to fit residues: 17.5471 Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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: 0.7470 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4410 Z= 0.186 Angle : 0.522 6.920 5996 Z= 0.266 Chirality : 0.038 0.137 711 Planarity : 0.004 0.053 733 Dihedral : 7.630 61.559 638 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.04 % Allowed : 21.96 % Favored : 75.00 % 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: 2.09 (0.37), residues: 552 helix: 2.71 (0.26), residues: 364 sheet: 0.47 (0.79), residues: 47 loop : -2.05 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.001 0.000 HIS A 112 PHE 0.012 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.476 Fit side-chains REVERT: A 248 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.6219 (m-70) REVERT: A 410 MET cc_start: 0.8314 (tmm) cc_final: 0.8075 (tmm) REVERT: B 108 SER cc_start: 0.8650 (m) cc_final: 0.8419 (m) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1458 time to fit residues: 11.8443 Evaluate side-chains 51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4410 Z= 0.253 Angle : 0.542 7.053 5996 Z= 0.276 Chirality : 0.038 0.136 711 Planarity : 0.004 0.055 733 Dihedral : 7.565 58.378 638 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.78 % Allowed : 21.09 % Favored : 74.13 % 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: 2.01 (0.37), residues: 552 helix: 2.62 (0.26), residues: 363 sheet: 0.65 (0.81), residues: 47 loop : -2.06 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.010 0.001 PHE A 361 TYR 0.011 0.001 TYR A 335 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.457 Fit side-chains REVERT: A 248 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6243 (m-70) outliers start: 22 outliers final: 16 residues processed: 64 average time/residue: 0.1719 time to fit residues: 14.1812 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 31 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4410 Z= 0.225 Angle : 0.541 9.647 5996 Z= 0.270 Chirality : 0.038 0.135 711 Planarity : 0.004 0.055 733 Dihedral : 7.486 56.521 638 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.91 % Allowed : 22.61 % Favored : 73.48 % 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: 2.01 (0.37), residues: 552 helix: 2.59 (0.26), residues: 362 sheet: 0.81 (0.81), residues: 47 loop : -1.99 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.005 0.001 HIS A 467 PHE 0.009 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.471 Fit side-chains REVERT: A 248 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6166 (m-70) REVERT: A 253 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.4227 (tp) outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.1617 time to fit residues: 13.0175 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4410 Z= 0.253 Angle : 0.551 8.512 5996 Z= 0.276 Chirality : 0.039 0.135 711 Planarity : 0.004 0.055 733 Dihedral : 7.447 58.672 638 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.70 % Allowed : 23.26 % Favored : 73.04 % 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: 1.95 (0.37), residues: 552 helix: 2.53 (0.26), residues: 362 sheet: 0.83 (0.81), residues: 47 loop : -1.99 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.009 0.001 PHE A 64 TYR 0.011 0.001 TYR A 335 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.490 Fit side-chains REVERT: A 248 HIS cc_start: 0.6758 (OUTLIER) cc_final: 0.6393 (m-70) REVERT: A 253 LEU cc_start: 0.4703 (OUTLIER) cc_final: 0.4460 (tp) REVERT: A 285 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7786 (mp) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.1638 time to fit residues: 14.0632 Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4410 Z= 0.257 Angle : 0.559 8.142 5996 Z= 0.279 Chirality : 0.039 0.136 711 Planarity : 0.004 0.056 733 Dihedral : 6.869 55.814 636 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.70 % Allowed : 23.70 % Favored : 72.61 % 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: 1.85 (0.37), residues: 552 helix: 2.45 (0.26), residues: 364 sheet: 0.86 (0.81), residues: 47 loop : -2.12 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.008 0.001 PHE A 361 TYR 0.011 0.001 TYR A 335 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.471 Fit side-chains REVERT: A 193 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (tpp) REVERT: A 248 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6491 (m-70) REVERT: A 253 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4722 (tp) REVERT: A 285 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7788 (mp) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.1673 time to fit residues: 13.8782 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4410 Z= 0.227 Angle : 0.549 8.033 5996 Z= 0.272 Chirality : 0.038 0.139 711 Planarity : 0.004 0.055 733 Dihedral : 6.485 56.837 636 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.26 % Allowed : 23.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.37), residues: 552 helix: 2.51 (0.26), residues: 363 sheet: 0.93 (0.82), residues: 47 loop : -2.16 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.009 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.437 Fit side-chains REVERT: A 248 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.6331 (m-70) REVERT: A 253 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4707 (tp) REVERT: A 285 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7786 (mp) outliers start: 15 outliers final: 12 residues processed: 61 average time/residue: 0.1708 time to fit residues: 13.4897 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4410 Z= 0.266 Angle : 0.571 7.969 5996 Z= 0.284 Chirality : 0.039 0.140 711 Planarity : 0.004 0.056 733 Dihedral : 6.394 57.010 636 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.48 % Allowed : 23.70 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.37), residues: 552 helix: 2.40 (0.26), residues: 364 sheet: 0.98 (0.82), residues: 47 loop : -2.17 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.008 0.001 PHE A 236 TYR 0.011 0.001 TYR A 335 ARG 0.002 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.470 Fit side-chains REVERT: A 248 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6387 (m-70) REVERT: A 253 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.4719 (tp) REVERT: A 285 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7795 (mp) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 0.1793 time to fit residues: 13.9395 Evaluate side-chains 61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.179473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.152007 restraints weight = 4371.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.149002 restraints weight = 6216.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148932 restraints weight = 6568.805| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4410 Z= 0.226 Angle : 0.553 7.974 5996 Z= 0.274 Chirality : 0.038 0.140 711 Planarity : 0.004 0.055 733 Dihedral : 5.685 46.702 633 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.26 % Allowed : 23.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.37), residues: 552 helix: 2.44 (0.26), residues: 364 sheet: 1.11 (0.82), residues: 47 loop : -2.21 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 467 PHE 0.009 0.001 PHE A 361 TYR 0.010 0.001 TYR A 459 ARG 0.002 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1110.99 seconds wall clock time: 20 minutes 59.45 seconds (1259.45 seconds total)