Starting phenix.real_space_refine on Fri Aug 22 13:16:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrv_18627/08_2025/8qrv_18627.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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 15 5.16 5 Na 1 4.78 5 C 2044 2.51 5 N 509 2.21 5 O 542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3111 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3110 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.26, per 1000 atoms: 0.41 Number of scatterers: 3111 At special positions: 0 Unit cell: (65.408, 62.342, 76.65, 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 15 16.00 Na 1 11.00 O 542 8.00 N 509 7.00 C 2044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 85.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 88.1% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.639A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 103 Proline residue: B 83 - end of helix Proline residue: B 92 - end of helix removed outlier: 3.877A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 155 through 158 removed outlier: 4.104A pdb=" N ALA B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.723A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 292 removed outlier: 3.510A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.753A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 6.401A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.517A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.506A pdb=" N THR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.766A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 426 removed outlier: 3.903A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.572A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 487 removed outlier: 3.907A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 209 260 hydrogen bonds defined for protein. 774 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: 0.47 Time building geometry restraints manager: 0.27 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: 985 1.34 - 1.46: 475 1.46 - 1.57: 1682 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 3166 Sorted by residual: bond pdb=" CG1 ILE B 417 " pdb=" CD1 ILE B 417 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CB ILE B 442 " pdb=" CG2 ILE B 442 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.64e-01 bond pdb=" CG LYS B 288 " pdb=" CD LYS B 288 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.42e-01 bond pdb=" CB ILE B 417 " pdb=" CG2 ILE B 417 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.07e-01 bond pdb=" CG1 ILE B 441 " pdb=" CD1 ILE B 441 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.79e-01 ... (remaining 3161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4257 1.96 - 3.93: 40 3.93 - 5.89: 15 5.89 - 7.85: 0 7.85 - 9.82: 1 Bond angle restraints: 4313 Sorted by residual: angle pdb=" C LEU B 284 " pdb=" N VAL B 285 " pdb=" CA VAL B 285 " ideal model delta sigma weight residual 122.35 117.81 4.54 1.18e+00 7.18e-01 1.48e+01 angle pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.87e+00 angle pdb=" N ASN B 447 " pdb=" CA ASN B 447 " pdb=" C ASN B 447 " ideal model delta sigma weight residual 108.63 112.35 -3.72 1.60e+00 3.91e-01 5.42e+00 angle pdb=" CA VAL B 459 " pdb=" CB VAL B 459 " pdb=" CG2 VAL B 459 " ideal model delta sigma weight residual 110.40 113.98 -3.58 1.70e+00 3.46e-01 4.43e+00 angle pdb=" N PHE B 91 " pdb=" CA PHE B 91 " pdb=" C PHE B 91 " ideal model delta sigma weight residual 113.45 116.28 -2.83 1.39e+00 5.18e-01 4.14e+00 ... (remaining 4308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1676 17.75 - 35.50: 134 35.50 - 53.25: 41 53.25 - 71.01: 4 71.01 - 88.76: 2 Dihedral angle restraints: 1857 sinusoidal: 676 harmonic: 1181 Sorted by residual: dihedral pdb=" CB GLU B 366 " pdb=" CG GLU B 366 " pdb=" CD GLU B 366 " pdb=" OE1 GLU B 366 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG B 101 " pdb=" CD ARG B 101 " pdb=" NE ARG B 101 " pdb=" CZ ARG B 101 " ideal model delta sinusoidal sigma weight residual -180.00 -135.85 -44.15 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual -180.00 -122.41 -57.59 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 452 0.056 - 0.111: 86 0.111 - 0.167: 2 0.167 - 0.222: 0 0.222 - 0.278: 1 Chirality restraints: 541 Sorted by residual: chirality pdb=" CB VAL B 459 " pdb=" CA VAL B 459 " pdb=" CG1 VAL B 459 " pdb=" CG2 VAL B 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO B 322 " pdb=" N PRO B 322 " pdb=" C PRO B 322 " pdb=" CB PRO B 322 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 538 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 258 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C PHE B 258 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE B 258 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 259 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 256 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE B 256 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE B 256 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 257 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 257 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ARG B 257 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 257 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 258 " 0.009 2.00e-02 2.50e+03 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1187 2.88 - 3.38: 3314 3.38 - 3.89: 5192 3.89 - 4.39: 5622 4.39 - 4.90: 9812 Nonbonded interactions: 25127 Sorted by model distance: nonbonded pdb=" O ASN B 386 " pdb="NA NA B 601 " model vdw 2.373 2.470 nonbonded pdb=" O GLY B 434 " pdb=" OG1 THR B 438 " model vdw 2.416 3.040 nonbonded pdb=" O THR B 350 " pdb=" OG SER B 351 " model vdw 2.428 3.040 nonbonded pdb=" O THR B 416 " pdb=" OG1 THR B 420 " model vdw 2.431 3.040 nonbonded pdb=" OE1 GLU B 179 " pdb=" OH TYR B 208 " model vdw 2.439 3.040 ... (remaining 25122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.980 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.045 3166 Z= 0.160 Angle : 0.570 9.816 4313 Z= 0.296 Chirality : 0.040 0.278 541 Planarity : 0.005 0.030 533 Dihedral : 14.311 88.757 1099 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.61 % Allowed : 15.55 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.43), residues: 413 helix: 1.72 (0.29), residues: 340 sheet: -1.51 (1.25), residues: 20 loop : 0.67 (0.87), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.006 0.001 TYR B 334 PHE 0.009 0.001 PHE B 184 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3166) covalent geometry : angle 0.56956 ( 4313) hydrogen bonds : bond 0.13617 ( 260) hydrogen bonds : angle 6.53886 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.137 Fit side-chains REVERT: B 136 LEU cc_start: 0.8492 (mp) cc_final: 0.8004 (tp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.3841 time to fit residues: 17.0991 Evaluate side-chains 38 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116906 restraints weight = 3710.036| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.89 r_work: 0.3307 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3166 Z= 0.183 Angle : 0.545 5.291 4313 Z= 0.279 Chirality : 0.040 0.130 541 Planarity : 0.004 0.033 533 Dihedral : 4.369 39.432 442 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.66 % Allowed : 14.94 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.43), residues: 413 helix: 2.17 (0.29), residues: 343 sheet: -1.72 (1.27), residues: 20 loop : 0.12 (0.91), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.010 0.001 TYR B 276 PHE 0.011 0.002 PHE B 184 TRP 0.007 0.001 TRP B 275 HIS 0.002 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3166) covalent geometry : angle 0.54505 ( 4313) hydrogen bonds : bond 0.05137 ( 260) hydrogen bonds : angle 4.79109 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.068 Fit side-chains REVERT: B 136 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8206 (tp) outliers start: 12 outliers final: 4 residues processed: 43 average time/residue: 0.3623 time to fit residues: 16.0979 Evaluate side-chains 37 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118943 restraints weight = 3653.901| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.90 r_work: 0.3338 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3166 Z= 0.135 Angle : 0.496 6.524 4313 Z= 0.251 Chirality : 0.038 0.171 541 Planarity : 0.004 0.031 533 Dihedral : 3.552 13.430 439 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.43), residues: 413 helix: 2.31 (0.28), residues: 346 sheet: -1.63 (1.31), residues: 20 loop : 0.48 (0.91), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.007 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.007 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3166) covalent geometry : angle 0.49618 ( 4313) hydrogen bonds : bond 0.04395 ( 260) hydrogen bonds : angle 4.47991 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.115 Fit side-chains REVERT: B 136 LEU cc_start: 0.8579 (mp) cc_final: 0.8183 (tp) outliers start: 7 outliers final: 2 residues processed: 46 average time/residue: 0.3954 time to fit residues: 18.7924 Evaluate side-chains 39 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117365 restraints weight = 3628.563| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.90 r_work: 0.3317 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3166 Z= 0.156 Angle : 0.502 5.336 4313 Z= 0.255 Chirality : 0.038 0.119 541 Planarity : 0.004 0.032 533 Dihedral : 3.555 13.555 439 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.66 % Allowed : 15.55 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.43), residues: 413 helix: 2.26 (0.28), residues: 346 sheet: -1.57 (1.32), residues: 20 loop : 0.45 (0.93), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.010 0.001 PHE B 184 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3166) covalent geometry : angle 0.50242 ( 4313) hydrogen bonds : bond 0.04661 ( 260) hydrogen bonds : angle 4.46575 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.134 Fit side-chains REVERT: B 136 LEU cc_start: 0.8566 (mp) cc_final: 0.8191 (tp) REVERT: B 475 ASP cc_start: 0.7492 (m-30) cc_final: 0.7243 (m-30) outliers start: 12 outliers final: 5 residues processed: 46 average time/residue: 0.3939 time to fit residues: 18.6568 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.0570 chunk 10 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.157556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121552 restraints weight = 3608.477| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.92 r_work: 0.3376 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3166 Z= 0.111 Angle : 0.485 8.143 4313 Z= 0.236 Chirality : 0.037 0.168 541 Planarity : 0.004 0.031 533 Dihedral : 3.392 13.157 439 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.74 % Allowed : 16.46 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.43), residues: 413 helix: 2.55 (0.28), residues: 341 sheet: -1.49 (1.34), residues: 20 loop : 0.24 (0.82), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 301 TYR 0.007 0.001 TYR B 334 PHE 0.008 0.001 PHE B 89 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3166) covalent geometry : angle 0.48461 ( 4313) hydrogen bonds : bond 0.03784 ( 260) hydrogen bonds : angle 4.27776 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.122 Fit side-chains REVERT: B 136 LEU cc_start: 0.8568 (mp) cc_final: 0.8145 (tp) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.3632 time to fit residues: 17.7159 Evaluate side-chains 41 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 263 ASN B 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118564 restraints weight = 3614.576| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.91 r_work: 0.3333 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3166 Z= 0.139 Angle : 0.508 6.728 4313 Z= 0.249 Chirality : 0.038 0.154 541 Planarity : 0.004 0.031 533 Dihedral : 3.426 12.846 439 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.66 % Allowed : 15.55 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.43), residues: 413 helix: 2.45 (0.28), residues: 341 sheet: -1.45 (1.36), residues: 20 loop : 0.45 (0.88), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.008 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3166) covalent geometry : angle 0.50833 ( 4313) hydrogen bonds : bond 0.04335 ( 260) hydrogen bonds : angle 4.34019 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.067 Fit side-chains REVERT: B 136 LEU cc_start: 0.8567 (mp) cc_final: 0.8187 (tp) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.3935 time to fit residues: 17.8076 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 2 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: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116735 restraints weight = 3702.048| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.93 r_work: 0.3292 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3166 Z= 0.160 Angle : 0.519 5.972 4313 Z= 0.258 Chirality : 0.039 0.146 541 Planarity : 0.004 0.032 533 Dihedral : 3.503 13.101 439 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.35 % Allowed : 15.55 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.43), residues: 413 helix: 2.38 (0.29), residues: 340 sheet: -1.35 (1.38), residues: 20 loop : 0.42 (0.90), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.012 0.001 TYR B 334 PHE 0.010 0.001 PHE B 184 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3166) covalent geometry : angle 0.51902 ( 4313) hydrogen bonds : bond 0.04692 ( 260) hydrogen bonds : angle 4.43165 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.073 Fit side-chains REVERT: B 136 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8045 (tp) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.3967 time to fit residues: 16.8124 Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117947 restraints weight = 3690.353| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.93 r_work: 0.3327 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3166 Z= 0.142 Angle : 0.511 5.883 4313 Z= 0.253 Chirality : 0.038 0.175 541 Planarity : 0.004 0.031 533 Dihedral : 3.481 13.342 439 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.05 % Allowed : 16.16 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.43), residues: 413 helix: 2.38 (0.29), residues: 340 sheet: -1.45 (1.37), residues: 20 loop : 0.40 (0.88), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.010 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3166) covalent geometry : angle 0.51113 ( 4313) hydrogen bonds : bond 0.04428 ( 260) hydrogen bonds : angle 4.37753 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.068 Fit side-chains REVERT: B 136 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8179 (tp) outliers start: 10 outliers final: 7 residues processed: 40 average time/residue: 0.3957 time to fit residues: 16.3372 Evaluate side-chains 42 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.154457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118151 restraints weight = 3677.522| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.93 r_work: 0.3324 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3166 Z= 0.142 Angle : 0.509 5.815 4313 Z= 0.252 Chirality : 0.038 0.169 541 Planarity : 0.004 0.031 533 Dihedral : 3.465 13.168 439 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.35 % Allowed : 15.85 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.43), residues: 413 helix: 2.36 (0.29), residues: 340 sheet: -1.50 (1.36), residues: 20 loop : 0.48 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3166) covalent geometry : angle 0.50916 ( 4313) hydrogen bonds : bond 0.04383 ( 260) hydrogen bonds : angle 4.36289 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.069 Fit side-chains REVERT: B 136 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8179 (tp) REVERT: B 444 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6697 (mt-10) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.4455 time to fit residues: 19.2368 Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117454 restraints weight = 3628.370| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.91 r_work: 0.3319 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3166 Z= 0.152 Angle : 0.518 5.540 4313 Z= 0.257 Chirality : 0.039 0.165 541 Planarity : 0.004 0.031 533 Dihedral : 3.498 13.166 439 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.05 % Allowed : 16.46 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.43), residues: 413 helix: 2.32 (0.29), residues: 340 sheet: -1.51 (1.36), residues: 20 loop : 0.54 (0.91), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.011 0.001 TYR B 334 PHE 0.009 0.001 PHE B 184 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3166) covalent geometry : angle 0.51831 ( 4313) hydrogen bonds : bond 0.04543 ( 260) hydrogen bonds : angle 4.40038 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.114 Fit side-chains REVERT: B 136 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8074 (tp) REVERT: B 444 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6685 (mt-10) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.4452 time to fit residues: 18.3110 Evaluate side-chains 43 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.156314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120168 restraints weight = 3680.257| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.93 r_work: 0.3350 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3166 Z= 0.126 Angle : 0.494 5.778 4313 Z= 0.243 Chirality : 0.038 0.170 541 Planarity : 0.004 0.031 533 Dihedral : 3.413 13.009 439 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.44 % Allowed : 17.38 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.43), residues: 413 helix: 2.44 (0.29), residues: 340 sheet: -1.48 (1.38), residues: 20 loop : 0.61 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.009 0.001 TYR B 334 PHE 0.009 0.001 PHE B 89 TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3166) covalent geometry : angle 0.49386 ( 4313) hydrogen bonds : bond 0.04056 ( 260) hydrogen bonds : angle 4.28982 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 968.95 seconds wall clock time: 17 minutes 16.89 seconds (1036.89 seconds total)