Starting phenix.real_space_refine on Wed Mar 5 20:38:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzr_36751/03_2025/8jzr_36751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzr_36751/03_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_36751/03_2025/8jzr_36751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzr_36751/03_2025/8jzr_36751.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzr_36751/03_2025/8jzr_36751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzr_36751/03_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-5624/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: 2.84, per 1000 atoms: 0.82 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: 0.90 Conformation dependent library (CDL) restraints added in 453.5 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: 0.33 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: 0.91 Time building geometry restraints manager: 1.07 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: 0.960 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: 0.020 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- 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 : 0.424 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: 0.2120 time to fit residues: 25.0067 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 : 0.368 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.1980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.162400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138247 restraints weight = 4269.390| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.93 r_work: 0.3449 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2187 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= 0.189 Angle : 0.577 5.904 4837 Z= 0.298 Chirality : 0.039 0.140 572 Planarity : 0.005 0.058 592 Dihedral : 4.103 16.953 504 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 1.42 % Allowed : 12.50 % 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: 1.55 (0.42), residues: 446 helix: 1.76 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.53 (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 362 PHE 0.022 0.001 PHE B 240 TYR 0.010 0.001 TYR B 113 ARG 0.004 0.001 ARG B 129 *********************** 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 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.368 Fit side-chains REVERT: B 320 LYS cc_start: 0.7788 (mttp) cc_final: 0.7395 (ptpt) REVERT: B 326 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 425 LYS cc_start: 0.6452 (ttmt) cc_final: 0.5848 (ttpt) REVERT: B 448 ASP cc_start: 0.7976 (t70) cc_final: 0.7484 (t0) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.1397 time to fit residues: 13.2081 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 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 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: 0.6980 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 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 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133378 restraints weight = 4256.669| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.94 r_work: 0.3410 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3557 Z= 0.195 Angle : 0.553 6.194 4837 Z= 0.283 Chirality : 0.038 0.144 572 Planarity : 0.004 0.056 592 Dihedral : 3.935 15.757 504 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % 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: 1.63 (0.41), residues: 446 helix: 1.88 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.24 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.001 0.001 HIS B 348 PHE 0.018 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.004 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 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.346 Fit side-chains REVERT: B 184 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8405 (ttpt) REVERT: B 240 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 320 LYS cc_start: 0.7862 (mttp) cc_final: 0.7447 (mttt) REVERT: B 326 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7954 (mp) REVERT: B 425 LYS cc_start: 0.6515 (ttmt) cc_final: 0.5797 (ttmt) REVERT: B 448 ASP cc_start: 0.7955 (t70) cc_final: 0.7421 (t0) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.1481 time to fit residues: 13.0864 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 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 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: 0.0570 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132840 restraints weight = 4320.984| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.95 r_work: 0.3399 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3075 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= 0.186 Angle : 0.538 6.102 4837 Z= 0.274 Chirality : 0.037 0.142 572 Planarity : 0.004 0.037 592 Dihedral : 3.817 14.268 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 3.41 % Allowed : 17.90 % Favored : 78.69 % 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: 1.83 (0.41), residues: 446 helix: 2.01 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.13 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS B 348 PHE 0.016 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.004 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 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 240 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: B 320 LYS cc_start: 0.7839 (mttp) cc_final: 0.7473 (mttp) REVERT: B 326 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 425 LYS cc_start: 0.6534 (ttmt) cc_final: 0.5981 (ttmt) REVERT: B 448 ASP cc_start: 0.7995 (t70) cc_final: 0.7433 (t0) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.1151 time to fit residues: 10.3341 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 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 380 LEU 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: 1.9990 chunk 19 optimal weight: 0.0020 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130462 restraints weight = 4353.871| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.10 r_work: 0.3336 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3557 Z= 0.194 Angle : 0.540 6.091 4837 Z= 0.274 Chirality : 0.037 0.142 572 Planarity : 0.004 0.037 592 Dihedral : 3.794 14.044 504 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.41 % Rotamer: Outliers : 2.56 % Allowed : 18.75 % Favored : 78.69 % 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: 1.99 (0.41), residues: 446 helix: 2.11 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -2.08 (0.62), residues: 90 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 0.018 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.005 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 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.397 Fit side-chains REVERT: B 240 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: B 320 LYS cc_start: 0.7728 (mttp) cc_final: 0.7527 (mttp) REVERT: B 326 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 425 LYS cc_start: 0.6385 (ttmt) cc_final: 0.5560 (ttmt) REVERT: B 448 ASP cc_start: 0.8067 (t70) cc_final: 0.7402 (t0) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.1339 time to fit residues: 10.9514 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 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 376 LEU 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: 0.9980 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 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 454 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132013 restraints weight = 4378.804| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.94 r_work: 0.3351 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3554 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 : 0.546 6.237 4837 Z= 0.274 Chirality : 0.037 0.141 572 Planarity : 0.004 0.038 592 Dihedral : 3.813 13.582 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.53 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: 2.21 (0.41), residues: 446 helix: 2.25 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.69 (0.63), 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 0.018 0.001 PHE B 240 TYR 0.013 0.001 TYR B 113 ARG 0.003 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: 12 poor density : 61 time to evaluate : 0.380 Fit side-chains REVERT: B 240 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: B 326 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 425 LYS cc_start: 0.6479 (ttmt) cc_final: 0.5690 (ttmt) REVERT: B 448 ASP cc_start: 0.8017 (t70) cc_final: 0.7352 (t0) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.1197 time to fit residues: 10.8451 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 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 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 40 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133087 restraints weight = 4301.149| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.00 r_work: 0.3396 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3557 Z= 0.167 Angle : 0.527 6.006 4837 Z= 0.266 Chirality : 0.037 0.140 572 Planarity : 0.003 0.038 592 Dihedral : 3.755 13.416 504 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.84 % Allowed : 19.60 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.41), residues: 446 helix: 2.19 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -2.12 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 453 HIS 0.001 0.000 HIS B 348 PHE 0.015 0.001 PHE B 240 TYR 0.009 0.001 TYR B 458 ARG 0.003 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: 10 poor density : 61 time to evaluate : 0.392 Fit side-chains REVERT: B 117 MET cc_start: 0.8620 (mmm) cc_final: 0.8388 (mmt) REVERT: B 240 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: B 326 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 425 LYS cc_start: 0.6484 (ttmt) cc_final: 0.5593 (ttpt) REVERT: B 448 ASP cc_start: 0.8020 (t70) cc_final: 0.7352 (t0) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.1394 time to fit residues: 11.8213 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 128 THR 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 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128511 restraints weight = 4293.542| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.04 r_work: 0.3336 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3557 Z= 0.252 Angle : 0.594 10.043 4837 Z= 0.296 Chirality : 0.039 0.150 572 Planarity : 0.004 0.038 592 Dihedral : 3.946 14.439 504 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: 2.11 (0.41), residues: 446 helix: 2.20 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.002 0.000 HIS B 348 PHE 0.023 0.002 PHE B 240 TYR 0.016 0.002 TYR B 113 ARG 0.002 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 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.336 Fit side-chains REVERT: B 82 MET cc_start: 0.8273 (mmt) cc_final: 0.8056 (mmt) REVERT: B 240 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: B 320 LYS cc_start: 0.7881 (mttm) cc_final: 0.7374 (mmtt) REVERT: B 326 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8188 (mp) REVERT: B 425 LYS cc_start: 0.6514 (ttmt) cc_final: 0.5758 (ttmt) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.1557 time to fit residues: 12.0344 Evaluate side-chains 59 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL 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: 0.7980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130109 restraints weight = 4235.595| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.95 r_work: 0.3345 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.033 3557 Z= 0.196 Angle : 0.569 9.626 4837 Z= 0.283 Chirality : 0.039 0.249 572 Planarity : 0.004 0.039 592 Dihedral : 3.841 13.273 504 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 19.89 % Favored : 76.99 % 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: 2.20 (0.41), residues: 446 helix: 2.26 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.73 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.001 0.000 HIS B 395 PHE 0.019 0.001 PHE B 240 TYR 0.011 0.001 TYR B 113 ARG 0.003 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 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.357 Fit side-chains REVERT: B 82 MET cc_start: 0.8246 (mmt) cc_final: 0.8033 (mmt) REVERT: B 240 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: B 326 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 425 LYS cc_start: 0.6458 (ttmt) cc_final: 0.5554 (ttpt) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.1419 time to fit residues: 10.9249 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129431 restraints weight = 4257.410| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.97 r_work: 0.3346 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 0.034 3557 Z= 0.200 Angle : 0.585 9.523 4837 Z= 0.287 Chirality : 0.040 0.251 572 Planarity : 0.004 0.039 592 Dihedral : 3.854 13.688 504 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: 2.17 (0.41), residues: 446 helix: 2.23 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.76 (0.61), 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 0.020 0.001 PHE B 240 TYR 0.012 0.001 TYR B 113 ARG 0.004 0.000 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 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 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.396 Fit side-chains REVERT: B 82 MET cc_start: 0.8242 (mmt) cc_final: 0.8027 (mmt) REVERT: B 240 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: B 326 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 425 LYS cc_start: 0.6443 (ttmt) cc_final: 0.5532 (ttpt) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1450 time to fit residues: 11.0444 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 326 LEU Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.153897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128267 restraints weight = 4350.423| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.99 r_work: 0.3335 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4032 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= 0.218 Angle : 0.602 11.255 4837 Z= 0.293 Chirality : 0.040 0.237 572 Planarity : 0.004 0.038 592 Dihedral : 3.884 13.894 504 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.12 % Allowed : 19.89 % Favored : 76.99 % 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: 2.15 (0.41), residues: 446 helix: 2.26 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 96 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 0.021 0.001 PHE B 240 TYR 0.012 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: 1993.34 seconds wall clock time: 34 minutes 51.67 seconds (2091.67 seconds total)