Starting phenix.real_space_refine on Fri May 9 14:20:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5y_38075/05_2025/8x5y_38075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5y_38075/05_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_38075/05_2025/8x5y_38075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5y_38075/05_2025/8x5y_38075.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5y_38075/05_2025/8x5y_38075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5y_38075/05_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-5687/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: 2.60, per 1000 atoms: 1.13 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: 0.63 Conformation dependent library (CDL) restraints added in 250.9 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: 0.19 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: 0.55 Time building geometry restraints manager: 0.70 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: 1.680 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.050 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:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- 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 2360 Z= 0.633 Angle : 0.901 16.410 3205 Z= 0.426 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 Details of bonding type rmsd hydrogen bonds : bond 0.11087 ( 153) hydrogen bonds : angle 5.48655 ( 456) SS BOND : bond 0.00262 ( 2) SS BOND : angle 2.82187 ( 4) covalent geometry : bond 0.01256 ( 2358) covalent geometry : angle 0.89560 ( 3201) *********************** 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 : 0.215 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 1.3435 time to fit residues: 37.2221 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 : 0.292 ------------------------------------------------------------------------------- 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 = 0.181474 restraints weight = 2702.404| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.68 r_work: 0.4001 rms_B_bonded: 3.64 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 2360 Z= 0.146 Angle : 0.664 7.146 3205 Z= 0.333 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 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 153) hydrogen bonds : angle 4.64959 ( 456) SS BOND : bond 0.00504 ( 2) SS BOND : angle 1.89890 ( 4) covalent geometry : bond 0.00326 ( 2358) covalent geometry : angle 0.66051 ( 3201) *********************** 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 : 0.256 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 1.3470 time to fit residues: 31.9627 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.195296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.177322 restraints weight = 2612.765| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.50 r_work: 0.3994 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4897 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2360 Z= 0.173 Angle : 0.664 7.072 3205 Z= 0.338 Chirality : 0.043 0.150 364 Planarity : 0.006 0.050 375 Dihedral : 9.268 94.478 317 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.41 % Allowed : 11.24 % Favored : 86.35 % 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: -0.50 (0.53), residues: 268 helix: 0.55 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -3.45 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 455 HIS 0.002 0.001 HIS B 448 PHE 0.010 0.001 PHE B 432 TYR 0.013 0.001 TYR B 135 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 153) hydrogen bonds : angle 4.67942 ( 456) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.89997 ( 4) covalent geometry : bond 0.00409 ( 2358) covalent geometry : angle 0.66106 ( 3201) *********************** 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 28 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.251 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 1.2808 time to fit residues: 31.6071 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 : 0.267 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.0170 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 overall best weight: 0.1414 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.200029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181933 restraints weight = 2596.359| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.56 r_work: 0.4044 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2360 Z= 0.127 Angle : 0.621 7.450 3205 Z= 0.308 Chirality : 0.041 0.122 364 Planarity : 0.005 0.041 375 Dihedral : 8.913 90.073 317 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.81 % Allowed : 10.44 % Favored : 86.75 % 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: -0.17 (0.54), residues: 268 helix: 0.79 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -3.35 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 189 HIS 0.003 0.001 HIS B 450 PHE 0.008 0.001 PHE B 432 TYR 0.012 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 153) hydrogen bonds : angle 4.38361 ( 456) SS BOND : bond 0.00450 ( 2) SS BOND : angle 1.50661 ( 4) covalent geometry : bond 0.00276 ( 2358) covalent geometry : angle 0.61877 ( 3201) *********************** 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 29 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.276 Fit side-chains REVERT: B 22 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6141 (ptp) REVERT: B 424 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.5154 (t80) outliers start: 7 outliers final: 2 residues processed: 25 average time/residue: 1.2383 time to fit residues: 31.8615 Evaluate side-chains 25 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.197144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178512 restraints weight = 2672.629| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.66 r_work: 0.4009 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2360 Z= 0.149 Angle : 0.640 7.810 3205 Z= 0.320 Chirality : 0.043 0.131 364 Planarity : 0.005 0.043 375 Dihedral : 9.046 90.296 317 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.02 % Allowed : 13.65 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.54), residues: 268 helix: 0.74 (0.37), residues: 208 sheet: None (None), residues: 0 loop : -3.32 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.002 0.001 HIS B 448 PHE 0.008 0.001 PHE B 432 TYR 0.014 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 153) hydrogen bonds : angle 4.44340 ( 456) SS BOND : bond 0.00440 ( 2) SS BOND : angle 1.68322 ( 4) covalent geometry : bond 0.00343 ( 2358) covalent geometry : angle 0.63786 ( 3201) *********************** 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 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 181 GLU cc_start: 0.4738 (pt0) cc_final: 0.4491 (pt0) REVERT: B 411 ARG cc_start: 0.3981 (mtt180) cc_final: 0.2824 (tmt170) REVERT: B 424 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.5213 (t80) outliers start: 10 outliers final: 3 residues processed: 28 average time/residue: 1.2732 time to fit residues: 36.6390 Evaluate side-chains 29 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.0000 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.2982 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.195937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.177729 restraints weight = 2667.221| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.56 r_work: 0.4006 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4888 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2360 Z= 0.155 Angle : 0.672 9.240 3205 Z= 0.334 Chirality : 0.043 0.133 364 Planarity : 0.005 0.044 375 Dihedral : 9.230 91.440 317 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.21 % Allowed : 16.47 % Favored : 80.32 % 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: -0.20 (0.54), residues: 268 helix: 0.80 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -3.34 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 455 HIS 0.002 0.001 HIS B 450 PHE 0.010 0.001 PHE B 432 TYR 0.016 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 153) hydrogen bonds : angle 4.48636 ( 456) SS BOND : bond 0.00503 ( 2) SS BOND : angle 1.71889 ( 4) covalent geometry : bond 0.00358 ( 2358) covalent geometry : angle 0.66920 ( 3201) *********************** 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 32 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.244 Fit side-chains REVERT: B 411 ARG cc_start: 0.3953 (mtt180) cc_final: 0.2829 (tmt170) REVERT: B 424 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.5139 (t80) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 1.2742 time to fit residues: 36.6844 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU 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 129 VAL 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: 0.6980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 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 = 0.4187 r_free = 0.4187 target = 0.185834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.166929 restraints weight = 2746.996| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.74 r_work: 0.3906 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2360 Z= 0.244 Angle : 0.826 10.152 3205 Z= 0.406 Chirality : 0.048 0.165 364 Planarity : 0.006 0.045 375 Dihedral : 9.546 95.797 317 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % 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: -0.71 (0.52), residues: 268 helix: 0.36 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -3.27 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 455 HIS 0.002 0.001 HIS B 448 PHE 0.013 0.002 PHE B 190 TYR 0.020 0.002 TYR B 135 ARG 0.002 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 153) hydrogen bonds : angle 4.92666 ( 456) SS BOND : bond 0.00597 ( 2) SS BOND : angle 2.26715 ( 4) covalent geometry : bond 0.00589 ( 2358) covalent geometry : angle 0.82239 ( 3201) *********************** 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 33 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.219 Fit side-chains REVERT: B 411 ARG cc_start: 0.4666 (mtt180) cc_final: 0.3520 (tmt170) REVERT: B 424 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5721 (t80) outliers start: 10 outliers final: 7 residues processed: 27 average time/residue: 1.2453 time to fit residues: 34.5848 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU 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 169 MET Chi-restraints excluded: chain B residue 424 PHE 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: 0.8980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.0980 overall best weight: 0.1756 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.196021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177663 restraints weight = 2725.179| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.62 r_work: 0.3995 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2360 Z= 0.136 Angle : 0.672 9.228 3205 Z= 0.328 Chirality : 0.042 0.128 364 Planarity : 0.005 0.041 375 Dihedral : 9.196 89.711 317 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.02 % Allowed : 17.27 % Favored : 78.71 % 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: -0.27 (0.54), residues: 268 helix: 0.75 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -3.35 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 189 HIS 0.003 0.001 HIS B 450 PHE 0.008 0.001 PHE B 432 TYR 0.017 0.001 TYR B 135 ARG 0.002 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 153) hydrogen bonds : angle 4.52161 ( 456) SS BOND : bond 0.00579 ( 2) SS BOND : angle 1.54499 ( 4) covalent geometry : bond 0.00299 ( 2358) covalent geometry : angle 0.67029 ( 3201) *********************** 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 33 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.269 Fit side-chains REVERT: B 181 GLU cc_start: 0.5026 (pt0) cc_final: 0.4777 (pt0) REVERT: B 411 ARG cc_start: 0.3959 (mtt180) cc_final: 0.3003 (ttp-170) REVERT: B 424 PHE cc_start: 0.5472 (OUTLIER) cc_final: 0.5211 (t80) outliers start: 10 outliers final: 4 residues processed: 28 average time/residue: 1.2792 time to fit residues: 36.7690 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 424 PHE 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: 0.6980 chunk 18 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.195013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176549 restraints weight = 2647.002| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.60 r_work: 0.3995 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4913 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2360 Z= 0.147 Angle : 0.740 11.652 3205 Z= 0.347 Chirality : 0.043 0.158 364 Planarity : 0.005 0.041 375 Dihedral : 9.078 90.117 317 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.61 % Allowed : 17.67 % Favored : 78.71 % 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: -0.20 (0.53), residues: 268 helix: 0.74 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.25 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 455 HIS 0.002 0.001 HIS B 450 PHE 0.008 0.001 PHE B 432 TYR 0.018 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 153) hydrogen bonds : angle 4.54027 ( 456) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.58662 ( 4) covalent geometry : bond 0.00335 ( 2358) covalent geometry : angle 0.73812 ( 3201) *********************** 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 32 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.248 Fit side-chains REVERT: B 411 ARG cc_start: 0.3927 (mtt180) cc_final: 0.2889 (ttp-170) REVERT: B 424 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.5142 (t80) outliers start: 9 outliers final: 5 residues processed: 26 average time/residue: 1.3569 time to fit residues: 36.1864 Evaluate side-chains 29 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 129 VAL 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: 0.0980 chunk 20 optimal weight: 0.0980 chunk 4 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.0070 chunk 17 optimal weight: 0.5980 overall best weight: 0.0716 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.202619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.184226 restraints weight = 2635.659| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.61 r_work: 0.4050 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4904 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2360 Z= 0.125 Angle : 0.663 9.368 3205 Z= 0.317 Chirality : 0.041 0.145 364 Planarity : 0.005 0.039 375 Dihedral : 9.055 88.338 317 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.01 % Allowed : 18.88 % 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: 0.01 (0.54), residues: 268 helix: 0.89 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -3.11 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 189 HIS 0.008 0.002 HIS B 450 PHE 0.006 0.001 PHE B 434 TYR 0.020 0.001 TYR B 135 ARG 0.001 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 153) hydrogen bonds : angle 4.34437 ( 456) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.23183 ( 4) covalent geometry : bond 0.00263 ( 2358) covalent geometry : angle 0.66149 ( 3201) ********************** 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 28 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.227 Fit side-chains REVERT: B 22 MET cc_start: 0.6340 (ptp) cc_final: 0.6109 (ptp) REVERT: B 181 GLU cc_start: 0.5069 (pt0) cc_final: 0.4838 (pt0) REVERT: B 411 ARG cc_start: 0.3904 (mtt180) cc_final: 0.3057 (ttp-170) REVERT: B 424 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.5211 (t80) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 1.3322 time to fit residues: 35.5433 Evaluate side-chains 27 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL 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: 0.4980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 26 optimal weight: 0.0010 chunk 23 optimal weight: 0.0010 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 overall best weight: 0.1392 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.201364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.182712 restraints weight = 2640.476| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.59 r_work: 0.4053 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2360 Z= 0.131 Angle : 0.717 12.174 3205 Z= 0.333 Chirality : 0.041 0.161 364 Planarity : 0.005 0.038 375 Dihedral : 8.995 88.289 317 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.61 % Allowed : 20.08 % 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: 0.09 (0.54), residues: 268 helix: 0.97 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -3.13 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 455 HIS 0.002 0.001 HIS B 450 PHE 0.007 0.001 PHE B 432 TYR 0.024 0.001 TYR B 135 ARG 0.001 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 153) hydrogen bonds : angle 4.33736 ( 456) SS BOND : bond 0.00468 ( 2) SS BOND : angle 1.31486 ( 4) covalent geometry : bond 0.00291 ( 2358) covalent geometry : angle 0.71603 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.14 seconds wall clock time: 35 minutes 47.09 seconds (2147.09 seconds total)