Starting phenix.real_space_refine on Wed Mar 5 20:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.map" model { file = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2025/7lck_23276.cif" } resolution = 3.24 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= 0.001 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 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 565 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 21 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: 3258 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 52 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 11} Link IDs: {None: 11} Time building chain proxies: 2.73, per 1000 atoms: 0.84 Number of scatterers: 3258 At special positions: 0 Unit cell: (60.8, 115.9, 69.35, 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 18 16.00 F 1 9.00 O 565 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.76 Conformation dependent library (CDL) restraints added in 385.4 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 67.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.690A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.791A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 removed outlier: 3.923A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 222 Processing helix chain 'R' and resid 224 through 256 removed outlier: 3.610A pdb=" N MET R 233 " --> pdb=" O VAL R 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 276 removed outlier: 4.025A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 280 through 292 removed outlier: 3.933A pdb=" N TRP R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 337 Proline residue: R 312 - end of helix removed outlier: 3.764A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 361 removed outlier: 4.317A pdb=" N ILE R 345 " --> pdb=" O CYS R 341 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS R 346 " --> pdb=" O LYS R 342 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 370 removed outlier: 3.578A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 391 removed outlier: 3.552A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.615A pdb=" N GLN R 410 " --> pdb=" O ASN R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.611A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.611A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 570 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: 0.83 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 980 1.41 - 1.54: 1857 1.54 - 1.68: 4 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.417 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.448 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CA SER R 392 " pdb=" CB SER R 392 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" C GLU R 387 " pdb=" O GLU R 387 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 4492 3.31 - 6.62: 64 6.62 - 9.93: 12 9.93 - 13.25: 2 13.25 - 16.56: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.97 104.88 9.09 1.28e+00 6.10e-01 5.04e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.85 121.54 -10.69 1.70e+00 3.46e-01 3.95e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 112.23 104.36 7.87 1.26e+00 6.30e-01 3.90e+01 angle pdb=" N TYR R 152 " pdb=" CA TYR R 152 " pdb=" C TYR R 152 " ideal model delta sigma weight residual 113.01 106.26 6.75 1.20e+00 6.94e-01 3.16e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 93.70 16.56 3.00e+00 1.11e-01 3.05e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 1701 16.60 - 33.20: 171 33.20 - 49.80: 51 49.80 - 66.40: 7 66.40 - 83.00: 2 Dihedral angle restraints: 1932 sinusoidal: 776 harmonic: 1156 Sorted by residual: dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -144.20 21.60 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual 122.80 141.04 -18.24 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 480 0.165 - 0.329: 14 0.329 - 0.493: 2 0.493 - 0.658: 0 0.658 - 0.822: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA PHE R 385 " pdb=" N PHE R 385 " pdb=" C PHE R 385 " pdb=" CB PHE R 385 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PHE R 367 " pdb=" N PHE R 367 " pdb=" C PHE R 367 " pdb=" CB PHE R 367 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 144 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU R 144 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU R 144 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR R 145 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ILE R 146 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 368 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ALA R 368 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA R 368 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE R 369 " 0.016 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 87 2.71 - 3.26: 3191 3.26 - 3.80: 4981 3.80 - 4.35: 6279 4.35 - 4.90: 10736 Nonbonded interactions: 25274 Sorted by model distance: nonbonded pdb=" NE2 GLN R 112 " pdb=" O SER R 117 " model vdw 2.160 3.120 nonbonded pdb=" O LEU R 244 " pdb=" ND2 ASN R 320 " model vdw 2.204 3.120 nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH2 ARG R 102 " model vdw 2.315 3.120 nonbonded pdb=" OG SER R 31 " pdb=" N LEU R 32 " model vdw 2.422 3.120 ... (remaining 25269 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.480 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.008 0.118 3351 Z= 0.522 Angle : 1.050 16.557 4571 Z= 0.664 Chirality : 0.075 0.822 497 Planarity : 0.006 0.040 557 Dihedral : 14.388 82.998 1172 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.16 % Allowed : 2.62 % Favored : 96.22 % Cbeta Deviations : 1.07 % 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: -0.93 (0.42), residues: 386 helix: -0.15 (0.32), residues: 265 sheet: 0.36 (2.04), residues: 10 loop : -1.62 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 PHE 0.020 0.002 PHE R 393 TYR 0.019 0.002 TYR R 242 ARG 0.003 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.354 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1774 time to fit residues: 9.7712 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0770 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.129731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105812 restraints weight = 5954.948| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.93 r_work: 0.3442 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.194 Angle : 0.638 11.231 4571 Z= 0.319 Chirality : 0.039 0.138 497 Planarity : 0.004 0.042 557 Dihedral : 6.228 36.790 458 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.58 % Allowed : 9.01 % Favored : 90.41 % 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: -0.02 (0.44), residues: 386 helix: 0.66 (0.33), residues: 267 sheet: 0.03 (1.88), residues: 10 loop : -1.59 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 284 HIS 0.002 0.000 HIS R 212 PHE 0.011 0.001 PHE R 393 TYR 0.032 0.002 TYR R 148 ARG 0.003 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.358 Fit side-chains REVERT: R 294 GLU cc_start: 0.7412 (pp20) cc_final: 0.7066 (pp20) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1646 time to fit residues: 6.6792 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103658 restraints weight = 5876.750| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.89 r_work: 0.3409 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3351 Z= 0.193 Angle : 0.572 8.839 4571 Z= 0.292 Chirality : 0.038 0.128 497 Planarity : 0.004 0.048 557 Dihedral : 5.543 34.348 455 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.58 % Allowed : 13.08 % Favored : 86.34 % 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 (0.44), residues: 386 helix: 1.09 (0.33), residues: 268 sheet: 0.02 (1.59), residues: 10 loop : -1.51 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 PHE 0.008 0.001 PHE R 156 TYR 0.028 0.002 TYR R 148 ARG 0.002 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.368 Fit side-chains REVERT: R 294 GLU cc_start: 0.7468 (pp20) cc_final: 0.6977 (pp20) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1529 time to fit residues: 5.5734 Evaluate side-chains 24 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103823 restraints weight = 5969.418| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.90 r_work: 0.3418 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.209 Angle : 0.570 8.183 4571 Z= 0.293 Chirality : 0.039 0.151 497 Planarity : 0.004 0.051 557 Dihedral : 5.437 34.658 453 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.87 % Allowed : 14.83 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.44), residues: 386 helix: 1.41 (0.33), residues: 262 sheet: 0.14 (1.46), residues: 10 loop : -1.48 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 284 HIS 0.001 0.000 HIS R 212 PHE 0.009 0.001 PHE R 156 TYR 0.027 0.002 TYR R 148 ARG 0.002 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.363 Fit side-chains REVERT: R 60 LEU cc_start: 0.9333 (mp) cc_final: 0.8995 (tp) REVERT: R 294 GLU cc_start: 0.7636 (pp20) cc_final: 0.7183 (pp20) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.1767 time to fit residues: 6.1454 Evaluate side-chains 23 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103407 restraints weight = 5964.614| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.84 r_work: 0.3421 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3351 Z= 0.206 Angle : 0.566 7.838 4571 Z= 0.291 Chirality : 0.038 0.124 497 Planarity : 0.004 0.052 557 Dihedral : 5.364 34.596 453 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.87 % Allowed : 15.41 % Favored : 83.72 % 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: 0.83 (0.44), residues: 386 helix: 1.35 (0.33), residues: 267 sheet: 0.14 (1.43), residues: 10 loop : -1.41 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 PHE 0.009 0.001 PHE R 156 TYR 0.027 0.002 TYR R 148 ARG 0.002 0.000 ARG R 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.331 Fit side-chains REVERT: R 60 LEU cc_start: 0.9329 (mp) cc_final: 0.9038 (tp) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.1441 time to fit residues: 5.3137 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 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 = 0.3868 r_free = 0.3868 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104429 restraints weight = 6057.459| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.86 r_work: 0.3429 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.184 Angle : 0.555 7.557 4571 Z= 0.286 Chirality : 0.038 0.121 497 Planarity : 0.005 0.055 557 Dihedral : 5.322 33.706 453 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.74 % Allowed : 15.70 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.44), residues: 386 helix: 1.52 (0.33), residues: 267 sheet: 0.47 (1.50), residues: 10 loop : -1.31 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 212 PHE 0.008 0.001 PHE R 156 TYR 0.026 0.001 TYR R 148 ARG 0.007 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.366 Fit side-chains REVERT: R 60 LEU cc_start: 0.9312 (mp) cc_final: 0.9035 (tp) REVERT: R 260 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.4489 (m-80) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.1436 time to fit residues: 5.1922 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 35 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.129676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105360 restraints weight = 5807.289| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.81 r_work: 0.3448 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3351 Z= 0.151 Angle : 0.540 7.351 4571 Z= 0.277 Chirality : 0.037 0.120 497 Planarity : 0.004 0.054 557 Dihedral : 5.142 32.721 453 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.45 % Allowed : 15.41 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.44), residues: 386 helix: 1.63 (0.33), residues: 269 sheet: 0.84 (1.64), residues: 10 loop : -1.50 (0.56), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 PHE 0.007 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.006 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9287 (mp) cc_final: 0.9050 (tp) REVERT: R 260 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4501 (m-80) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.1395 time to fit residues: 5.5035 Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.129121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.104760 restraints weight = 5898.600| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.81 r_work: 0.3440 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.184 Angle : 0.560 7.620 4571 Z= 0.284 Chirality : 0.038 0.121 497 Planarity : 0.004 0.055 557 Dihedral : 5.193 32.577 453 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.45 % Allowed : 15.70 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.44), residues: 386 helix: 1.67 (0.33), residues: 269 sheet: 1.05 (1.73), residues: 10 loop : -1.46 (0.57), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.008 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.003 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.411 Fit side-chains REVERT: R 60 LEU cc_start: 0.9271 (mp) cc_final: 0.9045 (tp) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.1884 time to fit residues: 7.0264 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.128803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104379 restraints weight = 5994.673| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.87 r_work: 0.3433 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3351 Z= 0.183 Angle : 0.553 7.369 4571 Z= 0.283 Chirality : 0.038 0.124 497 Planarity : 0.004 0.055 557 Dihedral : 5.131 32.495 453 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.87 % Allowed : 16.86 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.44), residues: 386 helix: 1.83 (0.33), residues: 262 sheet: 1.08 (1.77), residues: 10 loop : -1.48 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 PHE 0.008 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.002 0.000 ARG R 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9276 (mp) cc_final: 0.9053 (tp) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.1502 time to fit residues: 5.6573 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104611 restraints weight = 5836.816| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.82 r_work: 0.3433 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.195 Angle : 0.559 7.369 4571 Z= 0.288 Chirality : 0.038 0.148 497 Planarity : 0.004 0.055 557 Dihedral : 5.199 32.455 453 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.45 % Allowed : 16.57 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.44), residues: 386 helix: 1.82 (0.33), residues: 264 sheet: 0.94 (1.73), residues: 10 loop : -1.45 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.009 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.002 0.000 ARG R 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9259 (mp) cc_final: 0.9039 (tp) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.1558 time to fit residues: 5.4906 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.128981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.104591 restraints weight = 5899.758| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.85 r_work: 0.3434 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3351 Z= 0.180 Angle : 0.552 7.364 4571 Z= 0.284 Chirality : 0.037 0.123 497 Planarity : 0.004 0.055 557 Dihedral : 5.111 32.230 453 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.16 % Allowed : 16.57 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.44), residues: 386 helix: 1.88 (0.33), residues: 262 sheet: 0.76 (1.69), residues: 10 loop : -1.44 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 PHE 0.008 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.002 0.000 ARG R 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.98 seconds wall clock time: 31 minutes 49.82 seconds (1909.82 seconds total)