Starting phenix.real_space_refine on Mon Feb 10 23:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwi_27755/02_2025/8dwi_27755.cif" } resolution = 3.4 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= 0.018 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 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.97, per 1000 atoms: 0.93 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 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 14 16.00 O 536 8.00 N 504 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 373.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4313 1.28 - 2.56: 148 2.56 - 3.84: 28 3.84 - 5.12: 13 5.12 - 6.40: 5 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 3.040 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 3.120 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 3.120 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 3.120 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 3.120 ... (remaining 25849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.208 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 PHE 0.016 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.298 Fit side-chains REVERT: A 230 PHE cc_start: 0.4985 (m-80) cc_final: 0.4557 (m-10) REVERT: A 244 TRP cc_start: 0.3185 (t60) cc_final: 0.2467 (t60) REVERT: A 247 LEU cc_start: 0.6669 (mt) cc_final: 0.6219 (pp) REVERT: A 342 MET cc_start: 0.5783 (ttm) cc_final: 0.5446 (mtm) REVERT: A 432 PHE cc_start: 0.3628 (m-80) cc_final: 0.2892 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1689 time to fit residues: 11.4957 Evaluate side-chains 34 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.209940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176068 restraints weight = 4599.762| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.93 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4385 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3292 Z= 0.293 Angle : 0.764 6.870 4507 Z= 0.398 Chirality : 0.047 0.170 521 Planarity : 0.007 0.069 547 Dihedral : 5.253 18.884 448 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.18 % Allowed : 12.42 % Favored : 84.39 % 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: -0.95 (0.40), residues: 420 helix: -0.10 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.12 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 103 HIS 0.007 0.003 HIS A 183 PHE 0.034 0.003 PHE A 116 TYR 0.013 0.002 TYR A 421 ARG 0.010 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.303 Fit side-chains REVERT: A 227 THR cc_start: 0.5794 (p) cc_final: 0.5130 (p) REVERT: A 244 TRP cc_start: 0.3756 (t60) cc_final: 0.2926 (t60) REVERT: A 316 MET cc_start: 0.6499 (mpp) cc_final: 0.5895 (mmm) REVERT: A 438 MET cc_start: 0.6693 (tmm) cc_final: 0.5912 (ttm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.1265 time to fit residues: 9.0743 Evaluate side-chains 42 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.230030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.198750 restraints weight = 4285.707| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 3.19 r_work: 0.4225 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.6976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3292 Z= 0.271 Angle : 0.674 6.258 4507 Z= 0.351 Chirality : 0.043 0.154 521 Planarity : 0.006 0.067 547 Dihedral : 4.956 23.625 448 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 19.43 % Favored : 78.03 % 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: -0.68 (0.40), residues: 420 helix: 0.15 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.07 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 103 HIS 0.006 0.002 HIS A 414 PHE 0.020 0.002 PHE A 299 TYR 0.020 0.002 TYR A 203 ARG 0.009 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.304 Fit side-chains REVERT: A 117 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6780 (t80) REVERT: A 167 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6781 (tp) REVERT: A 466 ILE cc_start: 0.6353 (mm) cc_final: 0.6144 (mm) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1282 time to fit residues: 8.4571 Evaluate side-chains 45 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.224652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.192854 restraints weight = 4316.636| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 3.22 r_work: 0.4491 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.8642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3292 Z= 0.214 Angle : 0.623 6.018 4507 Z= 0.323 Chirality : 0.041 0.120 521 Planarity : 0.006 0.067 547 Dihedral : 4.771 20.841 448 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.78 % Allowed : 21.02 % Favored : 74.20 % 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: -0.65 (0.40), residues: 420 helix: 0.22 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.44 (0.56), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 226 HIS 0.009 0.002 HIS A 183 PHE 0.021 0.002 PHE A 322 TYR 0.011 0.001 TYR A 421 ARG 0.020 0.002 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 432 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 438 MET cc_start: 0.6860 (ttp) cc_final: 0.6640 (mtp) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 0.1327 time to fit residues: 9.4590 Evaluate side-chains 53 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.0070 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.211528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.179464 restraints weight = 4696.628| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.28 r_work: 0.4168 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.9818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3292 Z= 0.219 Angle : 0.635 8.969 4507 Z= 0.321 Chirality : 0.041 0.120 521 Planarity : 0.005 0.046 547 Dihedral : 4.730 18.500 448 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.14 % Allowed : 23.57 % Favored : 72.29 % 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: -0.48 (0.40), residues: 420 helix: 0.31 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.25 (0.55), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 226 HIS 0.007 0.002 HIS A 414 PHE 0.019 0.002 PHE A 322 TYR 0.008 0.001 TYR A 306 ARG 0.006 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.341 Fit side-chains REVERT: A 203 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 226 TRP cc_start: 0.6440 (p-90) cc_final: 0.6162 (p-90) REVERT: A 432 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6757 (t80) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.1084 time to fit residues: 8.3141 Evaluate side-chains 50 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.0070 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.220086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.186978 restraints weight = 4470.358| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 3.26 r_work: 0.4403 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 1.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3292 Z= 0.192 Angle : 0.625 6.596 4507 Z= 0.308 Chirality : 0.042 0.125 521 Planarity : 0.006 0.055 547 Dihedral : 4.795 22.168 448 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.46 % Allowed : 23.89 % Favored : 71.66 % 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: -0.55 (0.41), residues: 420 helix: 0.28 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.41 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.007 0.002 HIS A 414 PHE 0.019 0.001 PHE A 322 TYR 0.008 0.001 TYR A 117 ARG 0.014 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.322 Fit side-chains REVERT: A 182 MET cc_start: 0.5854 (tmm) cc_final: 0.5608 (tmm) REVERT: A 203 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7188 (t80) REVERT: A 432 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6791 (t80) outliers start: 14 outliers final: 7 residues processed: 59 average time/residue: 0.1209 time to fit residues: 9.2299 Evaluate side-chains 48 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.201917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.168125 restraints weight = 4905.645| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 3.69 r_work: 0.4152 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 1.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3292 Z= 0.238 Angle : 0.669 10.556 4507 Z= 0.328 Chirality : 0.044 0.203 521 Planarity : 0.006 0.057 547 Dihedral : 4.881 20.528 448 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.82 % Allowed : 25.80 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.41), residues: 420 helix: 0.33 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.20 (0.54), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 244 HIS 0.006 0.001 HIS A 414 PHE 0.021 0.002 PHE A 115 TYR 0.008 0.001 TYR A 203 ARG 0.007 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: 0.6282 (tmm) cc_final: 0.5891 (tmm) REVERT: A 189 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.7073 (m100) REVERT: A 203 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7178 (t80) REVERT: A 228 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5157 (t80) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1208 time to fit residues: 8.3155 Evaluate side-chains 49 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 228 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4519 r_free = 0.4519 target = 0.192574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.158442 restraints weight = 4974.391| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.53 r_work: 0.4059 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 1.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3292 Z= 0.293 Angle : 0.718 9.957 4507 Z= 0.365 Chirality : 0.046 0.187 521 Planarity : 0.006 0.053 547 Dihedral : 5.044 18.398 448 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.82 % Allowed : 24.20 % Favored : 71.97 % 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: -1.02 (0.40), residues: 420 helix: -0.03 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -2.45 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 339 HIS 0.006 0.002 HIS A 414 PHE 0.021 0.002 PHE A 116 TYR 0.014 0.001 TYR A 54 ARG 0.009 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7813 (m100) cc_final: 0.7599 (m100) REVERT: A 137 MET cc_start: 0.7127 (mpp) cc_final: 0.6794 (mmt) REVERT: A 175 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6999 (tm-30) REVERT: A 203 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.6858 (t80) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.1424 time to fit residues: 11.5926 Evaluate side-chains 61 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 33 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.0010 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.215823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.180047 restraints weight = 4536.799| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 3.60 r_work: 0.4345 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 1.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3292 Z= 0.195 Angle : 0.680 9.161 4507 Z= 0.332 Chirality : 0.043 0.157 521 Planarity : 0.006 0.054 547 Dihedral : 4.935 20.502 448 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.87 % Allowed : 27.71 % Favored : 69.43 % 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: -0.71 (0.40), residues: 420 helix: 0.19 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 244 HIS 0.011 0.002 HIS A 414 PHE 0.022 0.001 PHE A 322 TYR 0.008 0.001 TYR A 306 ARG 0.008 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7668 (m100) cc_final: 0.7373 (m100) REVERT: A 128 TYR cc_start: 0.7987 (t80) cc_final: 0.6798 (m-10) REVERT: A 137 MET cc_start: 0.6880 (mpp) cc_final: 0.6603 (mmt) REVERT: A 175 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7010 (tm-30) REVERT: A 189 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.5381 (t60) REVERT: A 203 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 226 TRP cc_start: 0.7058 (p-90) cc_final: 0.6473 (p-90) REVERT: A 250 ASP cc_start: 0.6696 (t0) cc_final: 0.6354 (t0) REVERT: A 284 PRO cc_start: 0.6542 (Cg_exo) cc_final: 0.6236 (Cg_endo) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.1310 time to fit residues: 10.6199 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 21 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.216118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.179626 restraints weight = 4505.863| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 3.59 r_work: 0.4001 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 1.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3292 Z= 0.193 Angle : 0.679 10.145 4507 Z= 0.330 Chirality : 0.042 0.176 521 Planarity : 0.006 0.055 547 Dihedral : 4.805 19.201 448 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.55 % Allowed : 29.62 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.40), residues: 420 helix: 0.28 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.10 (0.53), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 189 HIS 0.008 0.001 HIS A 414 PHE 0.022 0.001 PHE A 322 TYR 0.012 0.001 TYR A 117 ARG 0.008 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 110 TRP cc_start: 0.7813 (m100) cc_final: 0.7490 (m100) REVERT: A 128 TYR cc_start: 0.8017 (t80) cc_final: 0.6902 (m-10) REVERT: A 137 MET cc_start: 0.6935 (mpp) cc_final: 0.6719 (mmt) REVERT: A 182 MET cc_start: 0.6392 (tmm) cc_final: 0.6161 (tmm) REVERT: A 189 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.5076 (t60) REVERT: A 203 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 250 ASP cc_start: 0.6679 (t0) cc_final: 0.6287 (t0) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.1526 time to fit residues: 11.6150 Evaluate side-chains 60 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.210392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173834 restraints weight = 4565.559| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.54 r_work: 0.3965 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 1.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3292 Z= 0.211 Angle : 0.693 10.271 4507 Z= 0.341 Chirality : 0.043 0.181 521 Planarity : 0.006 0.055 547 Dihedral : 4.858 21.135 448 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 28.34 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.40), residues: 420 helix: 0.30 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.87 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 226 HIS 0.009 0.002 HIS A 414 PHE 0.022 0.002 PHE A 322 TYR 0.008 0.001 TYR A 54 ARG 0.008 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.95 seconds wall clock time: 33 minutes 18.49 seconds (1998.49 seconds total)