Starting phenix.real_space_refine on Wed Mar 5 15:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.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/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5y_38075/03_2025/8x5y_38075.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 21 5.16 5 C 1536 2.51 5 N 371 2.21 5 O 363 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2292 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2258 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 2 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XB7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 1.06 Number of scatterers: 2292 At special positions: 0 Unit cell: (55.12, 81.62, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 F 1 9.00 O 363 8.00 N 371 7.00 C 1536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " 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: 0.68 Conformation dependent library (CDL) restraints added in 266.6 milliseconds 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 532 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.794A pdb=" N VAL B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 removed outlier: 7.049A pdb=" N LYS B 57 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 79 removed outlier: 3.805A pdb=" N TYR B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.898A pdb=" N MET B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 removed outlier: 3.908A pdb=" N VAL B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.795A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASN B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N HIS B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 221 Proline residue: B 202 - end of helix removed outlier: 3.709A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 428 removed outlier: 5.252A pdb=" N LYS B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.567A pdb=" N PHE B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 468 removed outlier: 3.607A pdb=" N HIS B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Proline residue: B 465 - end of helix Processing helix chain 'B' and resid 472 through 480 removed outlier: 3.507A pdb=" N LYS B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) 153 hydrogen bonds defined for protein. 456 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: 0.60 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 320 1.30 - 1.43: 684 1.43 - 1.57: 1320 1.57 - 1.70: 1 1.70 - 1.84: 33 Bond restraints: 2358 Sorted by residual: bond pdb=" C14 XB7 B 601 " pdb=" N3 XB7 B 601 " ideal model delta sigma weight residual 1.374 1.565 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" C8 XB7 B 601 " pdb=" N1 XB7 B 601 " ideal model delta sigma weight residual 1.452 1.290 0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C22 XB7 B 601 " pdb=" C23 XB7 B 601 " ideal model delta sigma weight residual 1.387 1.549 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C21 XB7 B 601 " pdb=" C26 XB7 B 601 " ideal model delta sigma weight residual 1.391 1.551 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" C24 XB7 B 601 " pdb=" C25 XB7 B 601 " ideal model delta sigma weight residual 1.380 1.533 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 2353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 3151 3.28 - 6.56: 41 6.56 - 9.85: 8 9.85 - 13.13: 0 13.13 - 16.41: 1 Bond angle restraints: 3201 Sorted by residual: angle pdb=" C13 XB7 B 601 " pdb=" N4 XB7 B 601 " pdb=" C19 XB7 B 601 " ideal model delta sigma weight residual 106.37 122.78 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" N LEU B 136 " pdb=" CA LEU B 136 " pdb=" C LEU B 136 " ideal model delta sigma weight residual 114.62 109.41 5.21 1.14e+00 7.69e-01 2.09e+01 angle pdb=" N VAL B 437 " pdb=" CA VAL B 437 " pdb=" C VAL B 437 " ideal model delta sigma weight residual 113.39 108.24 5.15 1.47e+00 4.63e-01 1.23e+01 angle pdb=" C ILE B 115 " pdb=" CA ILE B 115 " pdb=" CB ILE B 115 " ideal model delta sigma weight residual 111.77 104.21 7.56 2.27e+00 1.94e-01 1.11e+01 angle pdb=" CA CYS B 444 " pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " ideal model delta sigma weight residual 114.40 121.06 -6.66 2.30e+00 1.89e-01 8.38e+00 ... (remaining 3196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.45: 1245 19.45 - 38.89: 112 38.89 - 58.34: 21 58.34 - 77.78: 3 77.78 - 97.22: 1 Dihedral angle restraints: 1382 sinusoidal: 565 harmonic: 817 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -42.89 -43.11 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CA ASN B 443 " pdb=" C ASN B 443 " pdb=" N CYS B 444 " pdb=" CA CYS B 444 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ARG B 411 " pdb=" C ARG B 411 " pdb=" N LYS B 412 " pdb=" CA LYS B 412 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 207 0.033 - 0.066: 107 0.066 - 0.098: 34 0.098 - 0.131: 12 0.131 - 0.164: 4 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA PRO B 29 " pdb=" N PRO B 29 " pdb=" C PRO B 29 " pdb=" CB PRO B 29 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA LEU B 201 " pdb=" N LEU B 201 " pdb=" C LEU B 201 " pdb=" CB LEU B 201 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 361 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 468 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B 469 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 201 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO B 202 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 197 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ILE B 197 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 197 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 198 " 0.012 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 798 2.86 - 3.37: 2246 3.37 - 3.88: 3644 3.88 - 4.39: 4127 4.39 - 4.90: 6979 Nonbonded interactions: 17794 Sorted by model distance: nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.346 3.040 nonbonded pdb=" O LYS B 477 " pdb=" NH1 ARG B 481 " model vdw 2.405 3.120 nonbonded pdb=" N ASP B 178 " pdb=" OD1 ASP B 178 " model vdw 2.470 3.120 nonbonded pdb=" OD1 ASP B 124 " pdb=" OH TYR B 135 " model vdw 2.478 3.040 nonbonded pdb=" O MET B 169 " pdb=" N GLN B 171 " model vdw 2.497 3.120 ... (remaining 17789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 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 : 0.013 0.191 2358 Z= 0.897 Angle : 0.896 16.410 3201 Z= 0.424 Chirality : 0.046 0.164 364 Planarity : 0.006 0.064 375 Dihedral : 14.802 97.225 844 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.40 % Allowed : 1.20 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.54), residues: 268 helix: 0.37 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -3.42 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 208 HIS 0.002 0.001 HIS B 59 PHE 0.008 0.001 PHE B 432 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.219 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 1.2473 time to fit residues: 34.5748 Evaluate side-chains 25 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.181473 restraints weight = 2702.403| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.68 r_work: 0.4001 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2358 Z= 0.208 Angle : 0.661 7.146 3201 Z= 0.332 Chirality : 0.043 0.143 364 Planarity : 0.006 0.051 375 Dihedral : 9.193 95.015 317 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.61 % Allowed : 7.63 % Favored : 90.76 % 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: -0.44 (0.54), residues: 268 helix: 0.66 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -3.50 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.001 0.001 HIS B 59 PHE 0.008 0.001 PHE B 432 TYR 0.012 0.001 TYR B 135 ARG 0.002 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.255 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 1.3664 time to fit residues: 32.5353 Evaluate side-chains 25 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.189330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170685 restraints weight = 2657.335| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.67 r_work: 0.3948 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4962 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2358 Z= 0.317 Angle : 0.720 7.412 3201 Z= 0.367 Chirality : 0.046 0.163 364 Planarity : 0.006 0.055 375 Dihedral : 9.456 95.622 317 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.21 % Allowed : 11.24 % Favored : 85.54 % 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: -0.72 (0.53), residues: 268 helix: 0.44 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -3.54 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 455 HIS 0.003 0.001 HIS B 448 PHE 0.012 0.001 PHE B 432 TYR 0.014 0.001 TYR B 135 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.187 Fit side-chains REVERT: B 436 MET cc_start: 0.4190 (mtm) cc_final: 0.3890 (mtm) outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 1.1236 time to fit residues: 28.9541 Evaluate side-chains 27 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.192010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174248 restraints weight = 2649.463| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.47 r_work: 0.3971 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5018 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2358 Z= 0.265 Angle : 0.707 7.722 3201 Z= 0.349 Chirality : 0.044 0.147 364 Planarity : 0.006 0.049 375 Dihedral : 9.269 93.223 317 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.21 % Allowed : 14.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.53), residues: 268 helix: 0.39 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.44 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 189 HIS 0.002 0.001 HIS B 448 PHE 0.011 0.001 PHE B 432 TYR 0.015 0.001 TYR B 135 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.300 Fit side-chains REVERT: B 424 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.5209 (t80) REVERT: B 436 MET cc_start: 0.3954 (mtm) cc_final: 0.3713 (mtm) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 1.1822 time to fit residues: 32.8690 Evaluate side-chains 30 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.189111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170412 restraints weight = 2716.858| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.67 r_work: 0.3950 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2358 Z= 0.274 Angle : 0.693 8.105 3201 Z= 0.347 Chirality : 0.044 0.146 364 Planarity : 0.006 0.049 375 Dihedral : 9.507 92.899 317 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.42 % Allowed : 15.66 % Favored : 79.92 % 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: -0.71 (0.53), residues: 268 helix: 0.37 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.38 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 189 HIS 0.003 0.001 HIS B 448 PHE 0.011 0.001 PHE B 432 TYR 0.018 0.001 TYR B 135 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.246 Fit side-chains REVERT: B 411 ARG cc_start: 0.3744 (mtt180) cc_final: 0.2675 (tmt170) REVERT: B 424 PHE cc_start: 0.5438 (OUTLIER) cc_final: 0.5102 (t80) outliers start: 11 outliers final: 7 residues processed: 27 average time/residue: 1.2506 time to fit residues: 34.7145 Evaluate side-chains 31 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.194836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.176893 restraints weight = 2682.465| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.50 r_work: 0.3996 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2358 Z= 0.207 Angle : 0.666 9.465 3201 Z= 0.326 Chirality : 0.042 0.127 364 Planarity : 0.005 0.044 375 Dihedral : 9.257 90.736 317 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.02 % Allowed : 16.87 % Favored : 79.12 % 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: -0.44 (0.54), residues: 268 helix: 0.64 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -3.43 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 189 HIS 0.002 0.001 HIS B 450 PHE 0.009 0.001 PHE B 432 TYR 0.015 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.240 Fit side-chains REVERT: B 411 ARG cc_start: 0.4019 (mtt180) cc_final: 0.2892 (tmt170) REVERT: B 424 PHE cc_start: 0.5474 (OUTLIER) cc_final: 0.5187 (t80) outliers start: 10 outliers final: 4 residues processed: 28 average time/residue: 1.2670 time to fit residues: 36.4428 Evaluate side-chains 28 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.0020 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 overall best weight: 0.2746 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.192165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173361 restraints weight = 2701.172| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.68 r_work: 0.3974 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2358 Z= 0.222 Angle : 0.706 10.223 3201 Z= 0.339 Chirality : 0.043 0.145 364 Planarity : 0.005 0.043 375 Dihedral : 9.154 91.016 317 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.02 % Allowed : 17.67 % Favored : 78.31 % 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: -0.41 (0.53), residues: 268 helix: 0.60 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -3.35 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 189 HIS 0.002 0.001 HIS B 450 PHE 0.009 0.001 PHE B 432 TYR 0.016 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.245 Fit side-chains REVERT: B 411 ARG cc_start: 0.3865 (mtt180) cc_final: 0.2768 (tmt170) REVERT: B 424 PHE cc_start: 0.5315 (OUTLIER) cc_final: 0.5062 (t80) REVERT: B 429 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4728 (tp) outliers start: 10 outliers final: 5 residues processed: 29 average time/residue: 1.2387 time to fit residues: 36.8971 Evaluate side-chains 31 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.187848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168349 restraints weight = 2747.401| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.77 r_work: 0.3926 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2358 Z= 0.291 Angle : 0.745 11.205 3201 Z= 0.360 Chirality : 0.045 0.159 364 Planarity : 0.006 0.044 375 Dihedral : 9.381 93.192 317 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.21 % Allowed : 18.47 % Favored : 78.31 % 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: -0.61 (0.53), residues: 268 helix: 0.46 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.40 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 455 HIS 0.003 0.001 HIS B 448 PHE 0.011 0.001 PHE B 432 TYR 0.020 0.001 TYR B 135 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.223 Fit side-chains REVERT: B 411 ARG cc_start: 0.4420 (mtt180) cc_final: 0.3325 (tmt170) REVERT: B 424 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.5450 (t80) REVERT: B 429 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.5127 (tp) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 1.1295 time to fit residues: 32.5377 Evaluate side-chains 31 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.193728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.175206 restraints weight = 2648.381| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.60 r_work: 0.3972 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4897 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2358 Z= 0.218 Angle : 0.728 11.824 3201 Z= 0.343 Chirality : 0.043 0.127 364 Planarity : 0.005 0.043 375 Dihedral : 9.084 90.178 317 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.21 % Allowed : 19.68 % Favored : 77.11 % 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: -0.39 (0.53), residues: 268 helix: 0.63 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.38 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 189 HIS 0.002 0.001 HIS B 448 PHE 0.008 0.001 PHE B 432 TYR 0.020 0.001 TYR B 135 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.223 Fit side-chains REVERT: B 411 ARG cc_start: 0.3913 (mtt180) cc_final: 0.2952 (ttp-170) REVERT: B 424 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.5182 (t80) outliers start: 8 outliers final: 4 residues processed: 27 average time/residue: 1.1918 time to fit residues: 33.0619 Evaluate side-chains 27 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.192567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174141 restraints weight = 2688.474| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.54 r_work: 0.3956 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2358 Z= 0.280 Angle : 0.755 12.645 3201 Z= 0.362 Chirality : 0.045 0.174 364 Planarity : 0.005 0.043 375 Dihedral : 9.271 91.709 317 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.41 % Allowed : 20.88 % Favored : 76.71 % 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: -0.53 (0.53), residues: 268 helix: 0.57 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -3.50 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 455 HIS 0.003 0.001 HIS B 448 PHE 0.010 0.001 PHE B 432 TYR 0.023 0.001 TYR B 135 ARG 0.001 0.000 ARG B 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 536 Ramachandran restraints generated. 268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.247 Fit side-chains REVERT: B 411 ARG cc_start: 0.4063 (mtt180) cc_final: 0.3035 (tmt170) REVERT: B 424 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.5256 (t80) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 1.2072 time to fit residues: 33.4959 Evaluate side-chains 29 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 444 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.1914 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.193889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.174827 restraints weight = 2684.812| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.69 r_work: 0.3986 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2358 Z= 0.207 Angle : 0.738 12.272 3201 Z= 0.347 Chirality : 0.042 0.132 364 Planarity : 0.005 0.044 375 Dihedral : 9.262 89.571 317 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.01 % Allowed : 21.69 % Favored : 76.31 % 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: -0.26 (0.54), residues: 268 helix: 0.72 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -3.34 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 189 HIS 0.001 0.000 HIS B 448 PHE 0.008 0.001 PHE B 432 TYR 0.025 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.43 seconds wall clock time: 34 minutes 11.16 seconds (2051.16 seconds total)