Starting phenix.real_space_refine on Wed Jun 4 15:58:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3f_41860/06_2025/8u3f_41860.cif" } resolution = 3.31 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= 0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2274 2.51 5 N 534 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3410 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 19, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 3.15, per 1000 atoms: 0.92 Number of scatterers: 3410 At special positions: 0 Unit cell: (58.1, 64.74, 86.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 585 8.00 N 534 7.00 C 2274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 387 " 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: 0.86 Conformation dependent library (CDL) restraints added in 409.9 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.555A pdb=" N LEU A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.635A pdb=" N ASP A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.506A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 224 Proline residue: A 215 - end of helix removed outlier: 3.712A pdb=" N GLY A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.648A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 311 removed outlier: 3.743A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 332 through 356 Processing helix chain 'A' and resid 359 through 384 Proline residue: A 375 - end of helix removed outlier: 3.614A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.636A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.712A pdb=" N PHE A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 452 through 478 Processing helix chain 'A' and resid 483 through 487 239 hydrogen bonds defined for protein. 702 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: 0.99 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 920 1.46 - 1.58: 1565 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3513 Sorted by residual: bond pdb=" CA VAL A 280 " pdb=" CB VAL A 280 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.50e-01 bond pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 9.44e-01 bond pdb=" CA ASN A 323 " pdb=" C ASN A 323 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.66e-01 bond pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 1.447 1.457 -0.011 1.18e-02 7.18e+03 8.22e-01 bond pdb=" CB VAL A 211 " pdb=" CG2 VAL A 211 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.47e-01 ... (remaining 3508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 4434 1.05 - 2.10: 286 2.10 - 3.15: 44 3.15 - 4.20: 21 4.20 - 5.25: 6 Bond angle restraints: 4791 Sorted by residual: angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C LEU A 447 " pdb=" N THR A 448 " pdb=" CA THR A 448 " ideal model delta sigma weight residual 122.89 120.51 2.38 1.12e+00 7.97e-01 4.51e+00 angle pdb=" CA THR A 153 " pdb=" C THR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 118.44 121.64 -3.20 1.59e+00 3.96e-01 4.05e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 109.34 113.48 -4.14 2.08e+00 2.31e-01 3.97e+00 angle pdb=" CA LEU A 289 " pdb=" C LEU A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 118.44 121.58 -3.14 1.59e+00 3.96e-01 3.91e+00 ... (remaining 4786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1771 16.48 - 32.95: 182 32.95 - 49.43: 30 49.43 - 65.90: 3 65.90 - 82.38: 1 Dihedral angle restraints: 1987 sinusoidal: 737 harmonic: 1250 Sorted by residual: dihedral pdb=" CA ASN A 323 " pdb=" C ASN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASN A 323 " pdb=" CB ASN A 323 " pdb=" CG ASN A 323 " pdb=" OD1 ASN A 323 " ideal model delta sinusoidal sigma weight residual -90.00 -152.99 62.99 2 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " pdb=" CE LYS A 278 " pdb=" NZ LYS A 278 " ideal model delta sinusoidal sigma weight residual -180.00 -136.68 -43.32 3 1.50e+01 4.44e-03 7.79e+00 ... (remaining 1984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 356 0.037 - 0.073: 148 0.073 - 0.110: 33 0.110 - 0.146: 6 0.146 - 0.183: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA PRO A 192 " pdb=" N PRO A 192 " pdb=" C PRO A 192 " pdb=" CB PRO A 192 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 541 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " 0.014 2.00e-02 2.50e+03 1.40e-02 3.45e+00 pdb=" CG PHE A 305 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 290 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 163 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.022 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3343 3.32 - 3.85: 5797 3.85 - 4.37: 6821 4.37 - 4.90: 11982 Nonbonded interactions: 28854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OE2 GLU A 175 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.286 3.040 nonbonded pdb=" O PRO A 192 " pdb=" NH2 ARG A 353 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 262 " model vdw 2.352 3.040 nonbonded pdb=" O ALA A 444 " pdb=" OG1 THR A 448 " model vdw 2.358 3.040 ... (remaining 28849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.040 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.005 0.038 3514 Z= 0.197 Angle : 0.625 5.254 4793 Z= 0.369 Chirality : 0.041 0.183 544 Planarity : 0.005 0.046 581 Dihedral : 12.988 82.377 1188 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.37), residues: 431 helix: -0.90 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -0.82 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.006 0.001 HIS A 298 PHE 0.032 0.002 PHE A 305 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.16164 ( 239) hydrogen bonds : angle 6.20821 ( 702) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.40530 ( 2) covalent geometry : bond 0.00462 ( 3513) covalent geometry : angle 0.62481 ( 4791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.332 Fit side-chains REVERT: A 256 LYS cc_start: 0.5750 (mmtt) cc_final: 0.4278 (tttp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1816 time to fit residues: 9.4768 Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103379 restraints weight = 3868.840| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.77 r_work: 0.3011 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3514 Z= 0.132 Angle : 0.545 5.317 4793 Z= 0.289 Chirality : 0.040 0.114 544 Planarity : 0.005 0.045 581 Dihedral : 4.250 20.124 463 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.55 % Allowed : 9.70 % Favored : 89.75 % 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 (0.40), residues: 431 helix: 0.61 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.12 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.011 0.001 PHE A 305 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 239) hydrogen bonds : angle 4.52928 ( 702) SS BOND : bond 0.00109 ( 1) SS BOND : angle 0.75713 ( 2) covalent geometry : bond 0.00284 ( 3513) covalent geometry : angle 0.54441 ( 4791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.324 Fit side-chains REVERT: A 256 LYS cc_start: 0.6166 (mmtt) cc_final: 0.3978 (tttp) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.1775 time to fit residues: 7.6994 Evaluate side-chains 32 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.137678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102823 restraints weight = 3872.001| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.76 r_work: 0.2998 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3514 Z= 0.155 Angle : 0.553 5.240 4793 Z= 0.288 Chirality : 0.041 0.115 544 Planarity : 0.005 0.043 581 Dihedral : 4.259 21.865 463 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 11.63 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.40), residues: 431 helix: 1.09 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.09 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.014 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 239) hydrogen bonds : angle 4.40446 ( 702) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.78913 ( 2) covalent geometry : bond 0.00368 ( 3513) covalent geometry : angle 0.55241 ( 4791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.354 Fit side-chains REVERT: A 256 LYS cc_start: 0.6187 (mmtt) cc_final: 0.4015 (tttp) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1972 time to fit residues: 8.9049 Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105393 restraints weight = 3883.914| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.77 r_work: 0.3029 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3514 Z= 0.115 Angle : 0.516 5.200 4793 Z= 0.268 Chirality : 0.039 0.113 544 Planarity : 0.005 0.041 581 Dihedral : 4.185 21.733 463 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 12.74 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.41), residues: 431 helix: 1.47 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.86 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.012 0.001 PHE A 51 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 239) hydrogen bonds : angle 4.25986 ( 702) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.82486 ( 2) covalent geometry : bond 0.00249 ( 3513) covalent geometry : angle 0.51608 ( 4791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.290 Fit side-chains REVERT: A 256 LYS cc_start: 0.6235 (mmtt) cc_final: 0.4046 (tttp) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1677 time to fit residues: 7.8983 Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104128 restraints weight = 3924.644| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.75 r_work: 0.3009 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.127 Angle : 0.523 5.212 4793 Z= 0.271 Chirality : 0.040 0.114 544 Planarity : 0.005 0.042 581 Dihedral : 4.146 22.331 463 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 14.13 % Favored : 83.93 % 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: 1.51 (0.41), residues: 431 helix: 1.62 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.73 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.004 0.001 HIS A 298 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 239) hydrogen bonds : angle 4.20996 ( 702) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.70327 ( 2) covalent geometry : bond 0.00293 ( 3513) covalent geometry : angle 0.52291 ( 4791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.374 Fit side-chains REVERT: A 256 LYS cc_start: 0.6189 (mmtt) cc_final: 0.4012 (tttp) REVERT: A 257 ARG cc_start: 0.8308 (mtm110) cc_final: 0.7702 (ttm110) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.1802 time to fit residues: 7.7345 Evaluate side-chains 33 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.4210 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.140975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105380 restraints weight = 3898.473| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.78 r_work: 0.3046 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3514 Z= 0.112 Angle : 0.507 5.181 4793 Z= 0.263 Chirality : 0.039 0.115 544 Planarity : 0.005 0.042 581 Dihedral : 4.070 22.187 463 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 13.85 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.41), residues: 431 helix: 1.82 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.71 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.032 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 239) hydrogen bonds : angle 4.14833 ( 702) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.69410 ( 2) covalent geometry : bond 0.00246 ( 3513) covalent geometry : angle 0.50728 ( 4791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.369 Fit side-chains REVERT: A 256 LYS cc_start: 0.6196 (mmtt) cc_final: 0.4002 (tttp) REVERT: A 257 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7650 (ttm110) REVERT: A 305 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6924 (t80) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.1471 time to fit residues: 6.9118 Evaluate side-chains 33 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 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 = 0.3597 r_free = 0.3597 target = 0.139412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104048 restraints weight = 3884.692| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.77 r_work: 0.3008 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3514 Z= 0.142 Angle : 0.531 5.215 4793 Z= 0.276 Chirality : 0.041 0.115 544 Planarity : 0.005 0.043 581 Dihedral : 4.123 22.287 463 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 15.24 % Favored : 82.83 % 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: 1.67 (0.41), residues: 431 helix: 1.73 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.66 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.026 0.001 PHE A 322 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 239) hydrogen bonds : angle 4.18858 ( 702) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.66509 ( 2) covalent geometry : bond 0.00338 ( 3513) covalent geometry : angle 0.53062 ( 4791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.329 Fit side-chains REVERT: A 256 LYS cc_start: 0.6252 (mmtt) cc_final: 0.4022 (tttp) REVERT: A 257 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7707 (ttm110) REVERT: A 305 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6998 (t80) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.1482 time to fit residues: 6.5291 Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 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 = 0.3597 r_free = 0.3597 target = 0.139423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103800 restraints weight = 3911.956| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.78 r_work: 0.3001 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3514 Z= 0.142 Angle : 0.531 5.226 4793 Z= 0.276 Chirality : 0.041 0.124 544 Planarity : 0.005 0.043 581 Dihedral : 4.149 22.483 463 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 15.24 % 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: 1.73 (0.41), residues: 431 helix: 1.78 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.64 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.024 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 239) hydrogen bonds : angle 4.19914 ( 702) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.63450 ( 2) covalent geometry : bond 0.00337 ( 3513) covalent geometry : angle 0.53109 ( 4791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.364 Fit side-chains REVERT: A 256 LYS cc_start: 0.6245 (mmtt) cc_final: 0.4032 (tttp) REVERT: A 305 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6946 (t80) outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 0.1550 time to fit residues: 6.6504 Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105061 restraints weight = 3801.324| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.77 r_work: 0.3020 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3514 Z= 0.121 Angle : 0.526 6.243 4793 Z= 0.270 Chirality : 0.040 0.124 544 Planarity : 0.005 0.043 581 Dihedral : 4.097 22.368 463 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 15.51 % 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: 1.89 (0.41), residues: 431 helix: 1.88 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.52 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.002 0.001 HIS A 298 PHE 0.022 0.001 PHE A 322 TYR 0.010 0.001 TYR A 306 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 239) hydrogen bonds : angle 4.15828 ( 702) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.59525 ( 2) covalent geometry : bond 0.00275 ( 3513) covalent geometry : angle 0.52645 ( 4791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.375 Fit side-chains REVERT: A 256 LYS cc_start: 0.6249 (mmtt) cc_final: 0.4009 (tttp) REVERT: A 257 ARG cc_start: 0.8297 (mtm110) cc_final: 0.7668 (ttm110) REVERT: A 305 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6974 (t80) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.1522 time to fit residues: 6.7617 Evaluate side-chains 36 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 16 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.1866 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110164 restraints weight = 3802.249| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.97 r_work: 0.3081 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3514 Z= 0.098 Angle : 0.503 5.998 4793 Z= 0.256 Chirality : 0.038 0.116 544 Planarity : 0.005 0.043 581 Dihedral : 3.973 22.575 463 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.94 % Allowed : 16.34 % Favored : 81.72 % 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: 2.16 (0.41), residues: 431 helix: 2.10 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.54 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 240 HIS 0.003 0.001 HIS A 298 PHE 0.021 0.001 PHE A 322 TYR 0.011 0.001 TYR A 306 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 239) hydrogen bonds : angle 4.06173 ( 702) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.52360 ( 2) covalent geometry : bond 0.00195 ( 3513) covalent geometry : angle 0.50330 ( 4791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.327 Fit side-chains REVERT: A 256 LYS cc_start: 0.6197 (mmtt) cc_final: 0.4049 (tttp) REVERT: A 257 ARG cc_start: 0.8250 (mtm110) cc_final: 0.7628 (ttm110) REVERT: A 305 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7032 (t80) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.1551 time to fit residues: 6.3941 Evaluate side-chains 33 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.140287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104638 restraints weight = 3878.382| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.79 r_work: 0.3016 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3514 Z= 0.151 Angle : 0.538 5.509 4793 Z= 0.276 Chirality : 0.041 0.127 544 Planarity : 0.005 0.044 581 Dihedral : 4.058 22.321 463 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 17.17 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.41), residues: 431 helix: 1.93 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.42 (0.61), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS A 298 PHE 0.020 0.001 PHE A 322 TYR 0.009 0.001 TYR A 306 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 239) hydrogen bonds : angle 4.13509 ( 702) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.54616 ( 2) covalent geometry : bond 0.00367 ( 3513) covalent geometry : angle 0.53770 ( 4791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.03 seconds wall clock time: 35 minutes 59.17 seconds (2159.17 seconds total)