Starting phenix.real_space_refine on Wed Mar 5 17:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.map" model { file = "/net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9joz_61690/03_2025/9joz_61690.cif" } resolution = 2.94 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= -0.001 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2104 2.51 5 N 515 2.21 5 O 514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain breaks: 2 Time building chain proxies: 2.60, per 1000 atoms: 0.83 Number of scatterers: 3143 At special positions: 0 Unit cell: (68, 65, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 514 8.00 N 515 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 424.3 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.569A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.696A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.861A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.280A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.508A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.391A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 264 through 294 removed outlier: 3.512A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.671A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 390 Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 419 Processing helix chain 'A' and resid 427 through 456 240 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 929 1.34 - 1.46: 799 1.46 - 1.58: 1487 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3231 Sorted by residual: bond pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" N LYS A 393 " pdb=" CA LYS A 393 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" CA SER A 138 " pdb=" CB SER A 138 " ideal model delta sigma weight residual 1.532 1.494 0.039 1.53e-02 4.27e+03 6.48e+00 bond pdb=" N SER A 73 " pdb=" CA SER A 73 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.80e+00 bond pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.74e+00 ... (remaining 3226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4217 1.07 - 2.13: 122 2.13 - 3.20: 49 3.20 - 4.27: 5 4.27 - 5.33: 6 Bond angle restraints: 4399 Sorted by residual: angle pdb=" N SER A 138 " pdb=" CA SER A 138 " pdb=" C SER A 138 " ideal model delta sigma weight residual 113.41 109.79 3.62 1.22e+00 6.72e-01 8.82e+00 angle pdb=" C PHE A 385 " pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " ideal model delta sigma weight residual 110.85 115.51 -4.66 1.70e+00 3.46e-01 7.50e+00 angle pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " pdb=" CG PHE A 385 " ideal model delta sigma weight residual 113.80 116.43 -2.63 1.00e+00 1.00e+00 6.93e+00 angle pdb=" CA LYS A 393 " pdb=" C LYS A 393 " pdb=" O LYS A 393 " ideal model delta sigma weight residual 120.89 118.02 2.87 1.10e+00 8.26e-01 6.80e+00 angle pdb=" O SER A 313 " pdb=" C SER A 313 " pdb=" N THR A 314 " ideal model delta sigma weight residual 122.07 124.68 -2.61 1.03e+00 9.43e-01 6.42e+00 ... (remaining 4394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1598 17.01 - 34.02: 187 34.02 - 51.03: 45 51.03 - 68.05: 15 68.05 - 85.06: 5 Dihedral angle restraints: 1850 sinusoidal: 702 harmonic: 1148 Sorted by residual: dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N VAL A 144 " pdb=" CA VAL A 144 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 85.06 -85.06 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 1847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 408 0.047 - 0.094: 90 0.094 - 0.141: 11 0.141 - 0.188: 3 0.188 - 0.235: 1 Chirality restraints: 513 Sorted by residual: chirality pdb=" CB VAL A 144 " pdb=" CA VAL A 144 " pdb=" CG1 VAL A 144 " pdb=" CG2 VAL A 144 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 140 " pdb=" CA ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CG2 ILE A 140 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 510 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 303 " -0.262 9.50e-02 1.11e+02 1.17e-01 8.45e+00 pdb=" NE ARG A 303 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 303 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 303 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 303 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 70 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 145 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 146 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.022 5.00e-02 4.00e+02 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 985 2.82 - 3.34: 3149 3.34 - 3.86: 5608 3.86 - 4.38: 6478 4.38 - 4.90: 10914 Nonbonded interactions: 27134 Sorted by model distance: nonbonded pdb=" O ILE A 339 " pdb=" OG1 THR A 343 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O GLN A 377 " model vdw 2.300 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.342 3.040 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.342 3.040 ... (remaining 27129 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: 1.100 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.030 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3231 Z= 0.199 Angle : 0.514 5.334 4399 Z= 0.312 Chirality : 0.040 0.235 513 Planarity : 0.007 0.117 526 Dihedral : 16.758 85.057 1112 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.89 % Allowed : 23.81 % Favored : 75.30 % 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: 1.34 (0.43), residues: 384 helix: 1.57 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.53 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 457 PHE 0.013 0.001 PHE A 84 TYR 0.010 0.001 TYR A 438 ARG 0.007 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.343 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 1.0063 time to fit residues: 35.6884 Evaluate side-chains 31 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.152123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115472 restraints weight = 3335.242| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.02 r_work: 0.2992 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3231 Z= 0.251 Angle : 0.502 5.552 4399 Z= 0.266 Chirality : 0.040 0.169 513 Planarity : 0.005 0.058 526 Dihedral : 5.450 59.832 439 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.27 % Allowed : 22.92 % Favored : 73.81 % 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: 1.69 (0.43), residues: 384 helix: 1.76 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.17 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.023 0.002 PHE A 84 TYR 0.015 0.001 TYR A 35 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.346 Fit side-chains REVERT: A 30 CYS cc_start: 0.8940 (m) cc_final: 0.8703 (m) REVERT: A 263 ARG cc_start: 0.7681 (tpt90) cc_final: 0.7097 (ttm-80) outliers start: 11 outliers final: 4 residues processed: 37 average time/residue: 1.1258 time to fit residues: 43.2002 Evaluate side-chains 32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.150680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114335 restraints weight = 3261.651| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.01 r_work: 0.2985 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3231 Z= 0.240 Angle : 0.491 5.421 4399 Z= 0.259 Chirality : 0.039 0.171 513 Planarity : 0.005 0.058 526 Dihedral : 4.795 57.525 437 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.08 % Allowed : 23.51 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.44), residues: 384 helix: 1.82 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.17 (0.74), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.004 0.001 HIS A 457 PHE 0.022 0.002 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.007 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.317 Fit side-chains REVERT: A 30 CYS cc_start: 0.8851 (m) cc_final: 0.8638 (m) REVERT: A 263 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7281 (tpp-160) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 1.2109 time to fit residues: 43.8883 Evaluate side-chains 34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.113989 restraints weight = 3324.250| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.04 r_work: 0.2996 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3231 Z= 0.208 Angle : 0.475 5.428 4399 Z= 0.251 Chirality : 0.038 0.125 513 Planarity : 0.005 0.056 526 Dihedral : 4.718 56.035 437 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.38 % Allowed : 24.11 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.44), residues: 384 helix: 1.92 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.27 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.350 Fit side-chains REVERT: A 25 TRP cc_start: 0.6189 (p90) cc_final: 0.5889 (p90) REVERT: A 59 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: A 263 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7274 (tpp-160) REVERT: A 456 ARG cc_start: 0.7394 (ptp-110) cc_final: 0.6465 (ttp80) outliers start: 8 outliers final: 4 residues processed: 37 average time/residue: 1.1676 time to fit residues: 44.8304 Evaluate side-chains 34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.163929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128127 restraints weight = 3326.299| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.03 r_work: 0.3019 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3231 Z= 0.183 Angle : 0.461 5.412 4399 Z= 0.242 Chirality : 0.037 0.125 513 Planarity : 0.004 0.056 526 Dihedral : 4.597 54.171 437 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.98 % Allowed : 22.92 % Favored : 74.11 % 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: 1.97 (0.44), residues: 384 helix: 2.01 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.34 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.018 0.001 PHE A 84 TYR 0.011 0.001 TYR A 139 ARG 0.007 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.331 Fit side-chains REVERT: A 59 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7543 (m-10) REVERT: A 262 LEU cc_start: 0.7336 (tp) cc_final: 0.7086 (mm) REVERT: A 456 ARG cc_start: 0.7219 (ptp-110) cc_final: 0.6449 (ttp80) outliers start: 10 outliers final: 5 residues processed: 38 average time/residue: 0.9816 time to fit residues: 38.7961 Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.147108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109851 restraints weight = 3337.684| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.04 r_work: 0.2980 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3231 Z= 0.229 Angle : 0.486 5.454 4399 Z= 0.256 Chirality : 0.038 0.125 513 Planarity : 0.005 0.055 526 Dihedral : 4.627 52.041 437 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.57 % Allowed : 22.92 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.44), residues: 384 helix: 1.95 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.22 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.022 0.002 PHE A 84 TYR 0.014 0.001 TYR A 35 ARG 0.007 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.356 Fit side-chains REVERT: A 26 ARG cc_start: 0.5202 (ptm160) cc_final: 0.4403 (ptm160) REVERT: A 263 ARG cc_start: 0.7735 (tpt90) cc_final: 0.7258 (tpp-160) REVERT: A 456 ARG cc_start: 0.7118 (ptp-110) cc_final: 0.6406 (ttp80) outliers start: 12 outliers final: 7 residues processed: 38 average time/residue: 1.1201 time to fit residues: 44.1385 Evaluate side-chains 35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.147552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110683 restraints weight = 3281.786| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.01 r_work: 0.2998 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3231 Z= 0.215 Angle : 0.477 5.474 4399 Z= 0.252 Chirality : 0.038 0.125 513 Planarity : 0.005 0.055 526 Dihedral : 4.594 51.739 437 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.27 % Allowed : 24.70 % Favored : 72.02 % 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 (0.44), residues: 384 helix: 1.96 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.26 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.000 HIS A 457 PHE 0.021 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.008 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.331 Fit side-chains REVERT: A 26 ARG cc_start: 0.5185 (ptm160) cc_final: 0.4519 (ptm160) REVERT: A 456 ARG cc_start: 0.7164 (ptp-110) cc_final: 0.6471 (ttp80) outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 1.1063 time to fit residues: 39.0343 Evaluate side-chains 35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 457 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.149348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112322 restraints weight = 3322.549| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.06 r_work: 0.3014 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3231 Z= 0.180 Angle : 0.465 5.458 4399 Z= 0.246 Chirality : 0.037 0.129 513 Planarity : 0.005 0.056 526 Dihedral : 4.537 51.221 437 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.27 % Allowed : 24.70 % Favored : 72.02 % 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: 2.00 (0.44), residues: 384 helix: 2.02 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.26 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.005 0.001 HIS A 457 PHE 0.018 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.008 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.311 Fit side-chains REVERT: A 59 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: A 262 LEU cc_start: 0.7304 (tp) cc_final: 0.7034 (mm) REVERT: A 456 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6400 (ttp80) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 1.0107 time to fit residues: 39.8782 Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112148 restraints weight = 3314.062| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.01 r_work: 0.3052 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3231 Z= 0.183 Angle : 0.467 5.460 4399 Z= 0.247 Chirality : 0.037 0.126 513 Planarity : 0.005 0.055 526 Dihedral : 4.510 50.467 437 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.98 % Allowed : 24.11 % Favored : 72.92 % 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: 1.97 (0.44), residues: 384 helix: 2.01 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.40 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.004 0.001 HIS A 457 PHE 0.018 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.009 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.308 Fit side-chains REVERT: A 26 ARG cc_start: 0.5174 (ptm160) cc_final: 0.4723 (ptm160) REVERT: A 262 LEU cc_start: 0.7374 (tp) cc_final: 0.7106 (mm) REVERT: A 456 ARG cc_start: 0.6893 (ptp-110) cc_final: 0.6356 (ttp80) outliers start: 10 outliers final: 7 residues processed: 36 average time/residue: 0.9845 time to fit residues: 36.9893 Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113093 restraints weight = 3257.523| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.01 r_work: 0.3043 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3231 Z= 0.170 Angle : 0.467 5.445 4399 Z= 0.246 Chirality : 0.037 0.126 513 Planarity : 0.005 0.056 526 Dihedral : 4.483 49.944 437 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.08 % Allowed : 25.00 % Favored : 72.92 % 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: 2.03 (0.44), residues: 384 helix: 2.05 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.38 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 457 PHE 0.017 0.001 PHE A 84 TYR 0.011 0.001 TYR A 139 ARG 0.009 0.001 ARG A 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.364 Fit side-chains REVERT: A 262 LEU cc_start: 0.7374 (tp) cc_final: 0.7106 (mm) REVERT: A 456 ARG cc_start: 0.6675 (ptp-110) cc_final: 0.6309 (ttp80) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.8867 time to fit residues: 32.5142 Evaluate side-chains 33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.2882 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.156133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119234 restraints weight = 3328.947| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.07 r_work: 0.3071 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3231 Z= 0.152 Angle : 0.451 5.419 4399 Z= 0.238 Chirality : 0.037 0.125 513 Planarity : 0.005 0.056 526 Dihedral : 4.373 48.789 437 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.38 % Allowed : 25.00 % Favored : 72.62 % 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: 2.19 (0.44), residues: 384 helix: 2.18 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.40 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 PHE 0.015 0.001 PHE A 84 TYR 0.011 0.001 TYR A 139 ARG 0.008 0.001 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.13 seconds wall clock time: 42 minutes 56.77 seconds (2576.77 seconds total)