Starting phenix.real_space_refine on Tue Feb 11 01:33:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzr_36751/02_2025/8jzr_36751.cif" } resolution = 3.25 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= 0.060 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 18 5.16 5 C 2304 2.51 5 N 562 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3474 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3460 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.02, per 1000 atoms: 0.87 Number of scatterers: 3474 At special positions: 0 Unit cell: (82.0652, 56.9432, 67.8294, 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 18 16.00 O 590 8.00 N 562 7.00 C 2304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 436 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 458.5 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 834 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 81.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 34 through 57 removed outlier: 3.501A pdb=" N GLY B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 4.034A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 212 removed outlier: 3.989A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.629A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.503A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.849A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 4.132A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 372 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.866A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.953A pdb=" N LYS B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.589A pdb=" N TYR B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 759 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: 0.92 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 525 1.30 - 1.43: 963 1.43 - 1.55: 2041 1.55 - 1.68: 1 1.68 - 1.81: 27 Bond restraints: 3557 Sorted by residual: bond pdb=" CA ALA B 35 " pdb=" C ALA B 35 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.32e-02 5.74e+03 4.17e+01 bond pdb=" CA ALA B 36 " pdb=" C ALA B 36 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.09e+01 bond pdb=" C ALA B 36 " pdb=" O ALA B 36 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.00e+01 bond pdb=" CA ALA B 31 " pdb=" C ALA B 31 " ideal model delta sigma weight residual 1.523 1.457 0.066 1.34e-02 5.57e+03 2.41e+01 bond pdb=" C CYS B 37 " pdb=" O CYS B 37 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.16e-02 7.43e+03 1.89e+01 ... (remaining 3552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4684 1.92 - 3.84: 117 3.84 - 5.75: 28 5.75 - 7.67: 6 7.67 - 9.59: 2 Bond angle restraints: 4837 Sorted by residual: angle pdb=" C GLY B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta sigma weight residual 121.86 131.24 -9.38 1.65e+00 3.67e-01 3.23e+01 angle pdb=" N ARG B 34 " pdb=" CA ARG B 34 " pdb=" C ARG B 34 " ideal model delta sigma weight residual 113.97 107.79 6.18 1.28e+00 6.10e-01 2.33e+01 angle pdb=" C ALA B 31 " pdb=" N GLY B 32 " pdb=" CA GLY B 32 " ideal model delta sigma weight residual 119.98 114.70 5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" N PHE B 30 " pdb=" CA PHE B 30 " pdb=" C PHE B 30 " ideal model delta sigma weight residual 110.80 101.21 9.59 2.13e+00 2.20e-01 2.03e+01 angle pdb=" CA CYS B 37 " pdb=" C CYS B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 117.02 122.14 -5.12 1.17e+00 7.31e-01 1.91e+01 ... (remaining 4832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1827 14.97 - 29.95: 184 29.95 - 44.92: 48 44.92 - 59.90: 6 59.90 - 74.87: 2 Dihedral angle restraints: 2067 sinusoidal: 766 harmonic: 1301 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.10 35.90 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA PRO B 390 " pdb=" C PRO B 390 " pdb=" N ILE B 391 " pdb=" CA ILE B 391 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" N ARG B 33 " pdb=" C ARG B 33 " pdb=" CA ARG B 33 " pdb=" CB ARG B 33 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 2064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 506 0.065 - 0.130: 54 0.130 - 0.196: 7 0.196 - 0.261: 4 0.261 - 0.326: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" CA CYS B 37 " pdb=" N CYS B 37 " pdb=" C CYS B 37 " pdb=" CB CYS B 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ALA B 31 " pdb=" N ALA B 31 " pdb=" C ALA B 31 " pdb=" CB ALA B 31 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PHE B 30 " pdb=" N PHE B 30 " pdb=" C PHE B 30 " pdb=" CB PHE B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 569 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 389 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.82e+00 pdb=" N PRO B 390 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 28 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C GLY B 28 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY B 28 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 29 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 187 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 188 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " -0.032 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1313 2.88 - 3.39: 3603 3.39 - 3.89: 5787 3.89 - 4.40: 6562 4.40 - 4.90: 11119 Nonbonded interactions: 28384 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" OG1 THR B 85 " model vdw 2.381 3.040 nonbonded pdb=" O GLN B 485 " pdb=" OG SER B 486 " model vdw 2.381 3.040 nonbonded pdb=" O ALA B 27 " pdb=" N ALA B 29 " model vdw 2.471 3.120 nonbonded pdb=" OD1 ASN B 436 " pdb=" ND1 HIS B 445 " model vdw 2.474 3.120 nonbonded pdb=" O ILE B 542 " pdb=" OG1 THR B 546 " model vdw 2.480 3.040 ... (remaining 28379 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: 0.720 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.007 0.085 3557 Z= 0.441 Angle : 0.772 9.589 4837 Z= 0.460 Chirality : 0.048 0.326 572 Planarity : 0.006 0.078 592 Dihedral : 12.737 74.870 1230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.81 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.75 (0.42), residues: 446 helix: 1.17 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 452 HIS 0.001 0.000 HIS B 348 PHE 0.020 0.001 PHE B 237 TYR 0.015 0.001 TYR B 335 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.401 Fit side-chains REVERT: B 502 VAL cc_start: 0.8649 (p) cc_final: 0.8417 (t) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2112 time to fit residues: 24.9259 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136370 restraints weight = 4286.785| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.94 r_work: 0.3430 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3557 Z= 0.213 Angle : 0.590 5.966 4837 Z= 0.303 Chirality : 0.039 0.142 572 Planarity : 0.005 0.058 592 Dihedral : 4.125 16.909 504 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 1.14 % Allowed : 12.78 % Favored : 86.08 % 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 (0.42), residues: 446 helix: 1.72 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.51 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.025 0.002 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.004 0.001 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.349 Fit side-chains REVERT: B 82 MET cc_start: 0.8168 (mmt) cc_final: 0.7943 (mmt) REVERT: B 320 LYS cc_start: 0.7813 (mttp) cc_final: 0.7449 (mttt) REVERT: B 326 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7811 (mp) REVERT: B 425 LYS cc_start: 0.6487 (ttmt) cc_final: 0.5760 (ttmt) REVERT: B 448 ASP cc_start: 0.8002 (t70) cc_final: 0.7517 (t0) REVERT: B 502 VAL cc_start: 0.8682 (p) cc_final: 0.8475 (t) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.1362 time to fit residues: 12.8751 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127647 restraints weight = 4285.261| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.96 r_work: 0.3335 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3557 Z= 0.270 Angle : 0.599 6.381 4837 Z= 0.306 Chirality : 0.039 0.146 572 Planarity : 0.005 0.056 592 Dihedral : 4.096 15.937 504 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.81 % Favored : 95.96 % Rotamer: Outliers : 4.55 % Allowed : 14.77 % Favored : 80.68 % 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: 1.61 (0.41), residues: 446 helix: 1.77 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.64 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.002 0.001 HIS B 348 PHE 0.025 0.002 PHE B 240 TYR 0.020 0.002 TYR B 113 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.347 Fit side-chains REVERT: B 240 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: B 326 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 425 LYS cc_start: 0.6549 (ttmt) cc_final: 0.5786 (ttmt) REVERT: B 448 ASP cc_start: 0.8015 (t70) cc_final: 0.7502 (t0) REVERT: B 454 GLN cc_start: 0.8523 (tt0) cc_final: 0.8273 (tt0) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.1239 time to fit residues: 11.1075 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 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 = 0.3721 r_free = 0.3721 target = 0.152897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127799 restraints weight = 4325.331| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.95 r_work: 0.3323 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3557 Z= 0.211 Angle : 0.551 6.151 4837 Z= 0.281 Chirality : 0.037 0.138 572 Planarity : 0.004 0.041 592 Dihedral : 3.992 14.195 504 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 3.41 % Allowed : 18.47 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.41), residues: 446 helix: 1.94 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.001 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.014 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.398 Fit side-chains REVERT: B 240 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 326 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 425 LYS cc_start: 0.6629 (ttmt) cc_final: 0.6083 (ttmt) REVERT: B 448 ASP cc_start: 0.8012 (t70) cc_final: 0.7471 (t0) outliers start: 12 outliers final: 7 residues processed: 67 average time/residue: 0.1386 time to fit residues: 12.0175 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128034 restraints weight = 4379.396| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.09 r_work: 0.3332 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3557 Z= 0.202 Angle : 0.539 6.095 4837 Z= 0.274 Chirality : 0.037 0.138 572 Planarity : 0.004 0.037 592 Dihedral : 3.960 14.203 504 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.12 % Allowed : 19.60 % Favored : 77.27 % 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: 1.86 (0.41), residues: 446 helix: 2.01 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.83 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.382 Fit side-chains REVERT: B 240 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: B 320 LYS cc_start: 0.8023 (mttp) cc_final: 0.7816 (mttm) REVERT: B 326 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8147 (mp) REVERT: B 425 LYS cc_start: 0.6524 (ttmt) cc_final: 0.6035 (ttpt) REVERT: B 448 ASP cc_start: 0.8040 (t70) cc_final: 0.7483 (t0) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1452 time to fit residues: 11.5482 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.154505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128839 restraints weight = 4384.490| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.00 r_work: 0.3322 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3557 Z= 0.203 Angle : 0.535 6.088 4837 Z= 0.272 Chirality : 0.037 0.137 572 Planarity : 0.004 0.038 592 Dihedral : 3.944 14.913 504 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.98 % Allowed : 18.18 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.41), residues: 446 helix: 2.07 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.83 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.324 Fit side-chains REVERT: B 181 ASP cc_start: 0.8764 (m-30) cc_final: 0.8518 (m-30) REVERT: B 240 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 326 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 425 LYS cc_start: 0.6480 (ttmt) cc_final: 0.5875 (ttmt) REVERT: B 448 ASP cc_start: 0.8054 (t70) cc_final: 0.7474 (t0) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.1435 time to fit residues: 12.1410 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.153351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127928 restraints weight = 4302.785| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.98 r_work: 0.3318 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3557 Z= 0.208 Angle : 0.540 6.123 4837 Z= 0.275 Chirality : 0.037 0.138 572 Planarity : 0.004 0.038 592 Dihedral : 3.956 14.249 504 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.69 % Allowed : 17.90 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.41), residues: 446 helix: 2.08 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.78 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.020 0.001 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.337 Fit side-chains REVERT: B 240 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: B 326 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 425 LYS cc_start: 0.6488 (ttmt) cc_final: 0.5714 (ttmt) REVERT: B 448 ASP cc_start: 0.8038 (t70) cc_final: 0.7445 (t0) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.1366 time to fit residues: 11.4513 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.154022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128905 restraints weight = 4262.947| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.96 r_work: 0.3340 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3557 Z= 0.194 Angle : 0.536 6.028 4837 Z= 0.274 Chirality : 0.037 0.135 572 Planarity : 0.004 0.037 592 Dihedral : 3.926 14.324 504 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 18.75 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.41), residues: 446 helix: 2.10 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.74 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.010 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: B 326 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 425 LYS cc_start: 0.6481 (ttmt) cc_final: 0.5577 (ttpt) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1386 time to fit residues: 11.8895 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.154957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130173 restraints weight = 4225.304| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.95 r_work: 0.3359 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3557 Z= 0.178 Angle : 0.526 5.962 4837 Z= 0.268 Chirality : 0.037 0.133 572 Planarity : 0.004 0.037 592 Dihedral : 3.860 13.529 504 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.98 % Allowed : 17.61 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.41), residues: 446 helix: 2.13 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.78 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.017 0.001 PHE B 240 TYR 0.009 0.001 TYR B 113 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: B 326 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 425 LYS cc_start: 0.6465 (ttmt) cc_final: 0.5868 (ttpt) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.1349 time to fit residues: 11.2621 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.155010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130123 restraints weight = 4227.222| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.94 r_work: 0.3360 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3557 Z= 0.178 Angle : 0.527 6.000 4837 Z= 0.269 Chirality : 0.037 0.134 572 Planarity : 0.004 0.037 592 Dihedral : 3.837 13.283 504 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.41 % Allowed : 18.18 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.41), residues: 446 helix: 2.14 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.78 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.018 0.001 PHE B 240 TYR 0.009 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: B 326 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 425 LYS cc_start: 0.6446 (ttmt) cc_final: 0.5856 (ttpt) outliers start: 12 outliers final: 9 residues processed: 64 average time/residue: 0.1305 time to fit residues: 10.8654 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 511 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.0050 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.153960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128790 restraints weight = 4340.560| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.97 r_work: 0.3341 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3557 Z= 0.196 Angle : 0.542 6.072 4837 Z= 0.276 Chirality : 0.037 0.136 572 Planarity : 0.004 0.037 592 Dihedral : 3.873 13.586 504 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 18.47 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.41), residues: 446 helix: 2.10 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.78 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS B 348 PHE 0.019 0.001 PHE B 240 TYR 0.010 0.001 TYR B 113 ARG 0.003 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.90 seconds wall clock time: 35 minutes 37.77 seconds (2137.77 seconds total)