Starting phenix.real_space_refine on Thu Nov 14 06:15:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfg_34720/11_2024/8hfg_34720.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.168 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 S 20 5.16 5 Cl 1 4.86 5 C 2950 2.51 5 N 679 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4366 Classifications: {'peptide': 545} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 525} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 28 Unusual residues: {' CL': 1, 'LDP': 2} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 3.27, per 1000 atoms: 0.74 Number of scatterers: 4394 At special positions: 0 Unit cell: (71.445, 68.1975, 96.3425, 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) Cl 1 17.00 S 20 16.00 O 744 8.00 N 679 7.00 C 2950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 1.26 Conformation dependent library (CDL) restraints added in 546.5 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 60 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.687A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.594A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 4.016A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.623A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.521A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.073A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.803A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.714A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.787A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.704A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.731A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.848A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.646A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.810A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 289 hydrogen bonds defined for protein. 843 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: 1.26 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 644 1.26 - 1.40: 1311 1.40 - 1.54: 2448 1.54 - 1.68: 96 1.68 - 1.81: 31 Bond restraints: 4530 Sorted by residual: bond pdb=" C LEU A 302 " pdb=" O LEU A 302 " ideal model delta sigma weight residual 1.236 1.121 0.115 1.31e-02 5.83e+03 7.71e+01 bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.134 0.100 1.35e-02 5.49e+03 5.53e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.47e-02 4.63e+03 3.82e+01 bond pdb=" C ARG A 301 " pdb=" O ARG A 301 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.32e-02 5.74e+03 3.38e+01 bond pdb=" C LYS A 88 " pdb=" O LYS A 88 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.16e-02 7.43e+03 3.33e+01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 6105 3.24 - 6.49: 59 6.49 - 9.73: 9 9.73 - 12.97: 3 12.97 - 16.22: 2 Bond angle restraints: 6178 Sorted by residual: angle pdb=" N LEU A 302 " pdb=" CA LEU A 302 " pdb=" C LEU A 302 " ideal model delta sigma weight residual 113.18 99.01 14.17 1.21e+00 6.83e-01 1.37e+02 angle pdb=" N TYR A 300 " pdb=" CA TYR A 300 " pdb=" C TYR A 300 " ideal model delta sigma weight residual 113.28 101.21 12.07 1.22e+00 6.72e-01 9.78e+01 angle pdb=" C ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta sigma weight residual 109.55 93.33 16.22 1.68e+00 3.54e-01 9.32e+01 angle pdb=" CA PRO A 83 " pdb=" N PRO A 83 " pdb=" CD PRO A 83 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.98e+01 angle pdb=" O TYR A 87 " pdb=" C TYR A 87 " pdb=" N LYS A 88 " ideal model delta sigma weight residual 122.09 113.75 8.34 1.08e+00 8.57e-01 5.97e+01 ... (remaining 6173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 2205 17.29 - 34.57: 237 34.57 - 51.86: 59 51.86 - 69.15: 16 69.15 - 86.44: 4 Dihedral angle restraints: 2521 sinusoidal: 945 harmonic: 1576 Sorted by residual: dihedral pdb=" C ARG A 301 " pdb=" N ARG A 301 " pdb=" CA ARG A 301 " pdb=" CB ARG A 301 " ideal model delta harmonic sigma weight residual -122.60 -103.73 -18.87 0 2.50e+00 1.60e-01 5.70e+01 dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.40 10.80 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 2518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 670 0.095 - 0.189: 14 0.189 - 0.284: 2 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA LYS A 88 " pdb=" N LYS A 88 " pdb=" C LYS A 88 " pdb=" CB LYS A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 684 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 93 " 0.026 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ALA A 93 " -0.092 2.00e-02 2.50e+03 pdb=" O ALA A 93 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE A 94 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 82 " 0.086 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 83 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 48 2.63 - 3.20: 4094 3.20 - 3.77: 6981 3.77 - 4.33: 9779 4.33 - 4.90: 16616 Nonbonded interactions: 37518 Sorted by model distance: nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 803 " model vdw 2.067 3.040 nonbonded pdb=" O PHE A 577 " pdb=" NH1 ARG A 587 " model vdw 2.146 3.120 nonbonded pdb=" O2 LDP A 701 " pdb=" O HOH A 801 " model vdw 2.253 3.040 nonbonded pdb=" NH1 ARG A 121 " pdb=" O ASN A 333 " model vdw 2.308 3.120 nonbonded pdb=" O GLY A 90 " pdb=" O HOH A 802 " model vdw 2.318 3.040 ... (remaining 37513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.310 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 0.131 4530 Z= 0.347 Angle : 0.804 16.218 6178 Z= 0.503 Chirality : 0.043 0.474 687 Planarity : 0.007 0.122 749 Dihedral : 15.709 86.436 1514 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.15 % Favored : 96.66 % Rotamer: Outliers : 1.96 % Allowed : 15.43 % Favored : 82.61 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.38), residues: 539 helix: 1.74 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.33 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.006 0.001 HIS A 296 PHE 0.021 0.001 PHE A 299 TYR 0.019 0.001 TYR A 300 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.472 Fit side-chains REVERT: A 300 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.5277 (m-10) outliers start: 9 outliers final: 2 residues processed: 86 average time/residue: 0.8765 time to fit residues: 79.5306 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 603 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4530 Z= 0.263 Angle : 0.632 7.739 6178 Z= 0.327 Chirality : 0.042 0.147 687 Planarity : 0.005 0.064 749 Dihedral : 6.278 71.975 595 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.91 % Allowed : 17.83 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.37), residues: 539 helix: 1.32 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 235 HIS 0.005 0.001 HIS A 199 PHE 0.021 0.002 PHE A 94 TYR 0.017 0.002 TYR A 84 ARG 0.004 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.464 Fit side-chains REVERT: A 375 ASN cc_start: 0.7728 (m-40) cc_final: 0.7449 (t0) REVERT: A 377 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 500 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7004 (ttp-170) REVERT: A 507 GLN cc_start: 0.8192 (tt0) cc_final: 0.7805 (tt0) REVERT: A 556 TRP cc_start: 0.7448 (m100) cc_final: 0.6459 (m-10) REVERT: A 595 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7085 (mt-10) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 0.7407 time to fit residues: 65.3615 Evaluate side-chains 68 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 43 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4530 Z= 0.193 Angle : 0.534 6.124 6178 Z= 0.268 Chirality : 0.039 0.145 687 Planarity : 0.004 0.051 749 Dihedral : 5.509 71.313 592 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.91 % Allowed : 18.91 % Favored : 77.17 % 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: 1.60 (0.37), residues: 539 helix: 1.56 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.01 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.005 0.001 HIS A 370 PHE 0.014 0.001 PHE A 110 TYR 0.017 0.001 TYR A 84 ARG 0.004 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.530 Fit side-chains REVERT: A 310 ASP cc_start: 0.7672 (m-30) cc_final: 0.7272 (m-30) REVERT: A 375 ASN cc_start: 0.8032 (m-40) cc_final: 0.7679 (t0) REVERT: A 377 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 403 PHE cc_start: 0.8343 (t80) cc_final: 0.8090 (t80) REVERT: A 500 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7100 (ttp-170) REVERT: A 507 GLN cc_start: 0.8196 (tt0) cc_final: 0.7815 (tt0) REVERT: A 556 TRP cc_start: 0.7753 (m100) cc_final: 0.6693 (m-10) outliers start: 18 outliers final: 6 residues processed: 81 average time/residue: 0.7022 time to fit residues: 60.6305 Evaluate side-chains 74 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4530 Z= 0.279 Angle : 0.584 8.100 6178 Z= 0.295 Chirality : 0.042 0.162 687 Planarity : 0.005 0.047 749 Dihedral : 5.270 57.321 590 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.57 % Allowed : 19.13 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.37), residues: 539 helix: 1.52 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.02 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.005 0.001 HIS A 372 PHE 0.031 0.002 PHE A 408 TYR 0.023 0.002 TYR A 271 ARG 0.002 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.484 Fit side-chains REVERT: A 500 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7132 (ttp-170) REVERT: A 507 GLN cc_start: 0.8289 (tt0) cc_final: 0.7792 (tt0) REVERT: A 556 TRP cc_start: 0.7989 (m100) cc_final: 0.6905 (m-10) outliers start: 21 outliers final: 9 residues processed: 67 average time/residue: 0.7464 time to fit residues: 53.2903 Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.7446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4530 Z= 0.249 Angle : 0.554 7.396 6178 Z= 0.280 Chirality : 0.040 0.176 687 Planarity : 0.004 0.045 749 Dihedral : 5.060 49.086 590 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.04 % Allowed : 20.43 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.37), residues: 539 helix: 1.51 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.03 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.003 0.001 HIS A 599 PHE 0.040 0.002 PHE A 408 TYR 0.021 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 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: 14 poor density : 56 time to evaluate : 0.708 Fit side-chains REVERT: A 500 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7158 (ttp-170) REVERT: A 507 GLN cc_start: 0.8276 (tt0) cc_final: 0.7818 (tt0) REVERT: A 541 LYS cc_start: 0.7574 (mtpt) cc_final: 0.6971 (mmmt) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.7926 time to fit residues: 56.5252 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 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: 0.7856 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4530 Z= 0.205 Angle : 0.536 8.091 6178 Z= 0.268 Chirality : 0.039 0.182 687 Planarity : 0.004 0.046 749 Dihedral : 4.835 43.973 590 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.26 % Allowed : 20.87 % Favored : 75.87 % 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: 1.64 (0.37), residues: 539 helix: 1.57 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.05 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 599 PHE 0.048 0.001 PHE A 408 TYR 0.019 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.515 Fit side-chains REVERT: A 174 THR cc_start: 0.8401 (m) cc_final: 0.8024 (p) REVERT: A 418 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: A 500 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7168 (ttp-170) REVERT: A 507 GLN cc_start: 0.8281 (tt0) cc_final: 0.7827 (tt0) REVERT: A 588 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mm) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.8491 time to fit residues: 57.6440 Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.7656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4530 Z= 0.218 Angle : 0.542 7.535 6178 Z= 0.272 Chirality : 0.039 0.164 687 Planarity : 0.004 0.044 749 Dihedral : 4.703 43.731 590 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.04 % Allowed : 21.09 % Favored : 75.87 % 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: 1.65 (0.37), residues: 539 helix: 1.55 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.13 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 404 HIS 0.003 0.001 HIS A 599 PHE 0.042 0.001 PHE A 408 TYR 0.020 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 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: 14 poor density : 52 time to evaluate : 0.482 Fit side-chains REVERT: A 174 THR cc_start: 0.8378 (m) cc_final: 0.8016 (p) REVERT: A 418 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: A 500 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7169 (ttp-170) REVERT: A 507 GLN cc_start: 0.8278 (tt0) cc_final: 0.7827 (tt0) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.7997 time to fit residues: 52.6983 Evaluate side-chains 60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4530 Z= 0.224 Angle : 0.545 7.505 6178 Z= 0.274 Chirality : 0.040 0.204 687 Planarity : 0.004 0.042 749 Dihedral : 4.695 44.287 590 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 22.83 % 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: 1.65 (0.37), residues: 539 helix: 1.53 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.18 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 404 HIS 0.003 0.001 HIS A 599 PHE 0.040 0.002 PHE A 408 TYR 0.020 0.001 TYR A 391 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.507 Fit side-chains REVERT: A 174 THR cc_start: 0.8406 (m) cc_final: 0.8028 (p) REVERT: A 403 PHE cc_start: 0.8090 (t80) cc_final: 0.7848 (t80) REVERT: A 418 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: A 500 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7160 (ttp-170) REVERT: A 507 GLN cc_start: 0.8278 (tt0) cc_final: 0.7827 (tt0) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.7799 time to fit residues: 50.6433 Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4530 Z= 0.173 Angle : 0.512 6.989 6178 Z= 0.258 Chirality : 0.039 0.168 687 Planarity : 0.004 0.043 749 Dihedral : 4.606 49.204 590 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.61 % Allowed : 22.83 % 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: 1.80 (0.37), residues: 539 helix: 1.65 (0.27), residues: 380 sheet: None (None), residues: 0 loop : 0.24 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 517 HIS 0.003 0.001 HIS A 599 PHE 0.036 0.001 PHE A 408 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.485 Fit side-chains REVERT: A 174 THR cc_start: 0.8309 (m) cc_final: 0.7924 (p) REVERT: A 403 PHE cc_start: 0.8033 (t80) cc_final: 0.7787 (t80) REVERT: A 418 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: A 500 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7140 (ttp-170) REVERT: A 507 GLN cc_start: 0.8230 (tt0) cc_final: 0.7884 (tt0) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.6542 time to fit residues: 49.9708 Evaluate side-chains 66 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4530 Z= 0.243 Angle : 0.560 7.657 6178 Z= 0.279 Chirality : 0.041 0.187 687 Planarity : 0.004 0.043 749 Dihedral : 4.665 43.473 590 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 22.61 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.37), residues: 539 helix: 1.53 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.30 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 PHE 0.036 0.002 PHE A 408 TYR 0.021 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 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: 12 poor density : 55 time to evaluate : 0.497 Fit side-chains REVERT: A 174 THR cc_start: 0.8469 (m) cc_final: 0.8096 (p) REVERT: A 403 PHE cc_start: 0.8081 (t80) cc_final: 0.7851 (t80) REVERT: A 418 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: A 500 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7140 (ttp-170) REVERT: A 507 GLN cc_start: 0.8290 (tt0) cc_final: 0.7836 (tt0) REVERT: A 556 TRP cc_start: 0.8025 (m100) cc_final: 0.6933 (m-10) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.7634 time to fit residues: 51.2956 Evaluate side-chains 64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 296 HIS A 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115311 restraints weight = 4709.575| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.29 r_work: 0.3125 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4530 Z= 0.248 Angle : 0.566 7.471 6178 Z= 0.284 Chirality : 0.041 0.185 687 Planarity : 0.004 0.043 749 Dihedral : 4.699 43.944 590 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.83 % Allowed : 22.17 % 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: 1.61 (0.37), residues: 539 helix: 1.46 (0.27), residues: 379 sheet: None (None), residues: 0 loop : 0.30 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 599 PHE 0.037 0.002 PHE A 408 TYR 0.021 0.001 TYR A 84 ARG 0.001 0.000 ARG A 121 =============================================================================== Job complete usr+sys time: 1744.67 seconds wall clock time: 32 minutes 22.68 seconds (1942.68 seconds total)