Starting phenix.real_space_refine on Sat Apr 26 22:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.map" model { file = "/net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y66_38968/04_2025/8y66_38968.cif" } resolution = 3.28 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= 0.008 sd= 0.100 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 15 5.16 5 C 2385 2.51 5 N 580 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3606 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3586 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.79 Number of scatterers: 3606 At special positions: 0 Unit cell: (83.3525, 63.8675, 70.3625, 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 15 16.00 O 626 8.00 N 580 7.00 C 2385 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: 1.02 Conformation dependent library (CDL) restraints added in 451.6 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 89.5% 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 54 through 76 removed outlier: 4.222A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 102 through 136 removed outlier: 4.716A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.774A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.647A pdb=" N GLY A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.454A pdb=" N VAL A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.930A pdb=" N GLU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 331 through 346 removed outlier: 6.386A pdb=" N ASN A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 352 through 379 removed outlier: 4.010A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.942A pdb=" N LEU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 3.570A pdb=" N LEU A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.668A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 removed outlier: 3.546A pdb=" N GLY A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 480 through 498 removed outlier: 4.527A pdb=" N PHE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.652A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 831 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: 0.98 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 548 1.31 - 1.44: 1011 1.44 - 1.56: 2116 1.56 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3697 Sorted by residual: bond pdb=" CAS AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.350 1.494 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CAJ AGI A 601 " pdb=" CAQ AGI A 601 " ideal model delta sigma weight residual 1.354 1.485 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" CAO AGI A 601 " pdb=" OAD AGI A 601 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CAQ AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.341 1.461 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAM AGI A 601 " pdb=" OAB AGI A 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 3692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 4912 2.07 - 4.14: 94 4.14 - 6.21: 23 6.21 - 8.29: 7 8.29 - 10.36: 2 Bond angle restraints: 5038 Sorted by residual: angle pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " pdb=" CG PHE A 235 " ideal model delta sigma weight residual 113.80 121.43 -7.63 1.00e+00 1.00e+00 5.83e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 112.59 104.30 8.29 1.22e+00 6.72e-01 4.61e+01 angle pdb=" C LEU A 234 " pdb=" N PHE A 235 " pdb=" CA PHE A 235 " ideal model delta sigma weight residual 122.67 112.31 10.36 1.59e+00 3.96e-01 4.24e+01 angle pdb=" N LEU A 234 " pdb=" CA LEU A 234 " pdb=" C LEU A 234 " ideal model delta sigma weight residual 112.90 104.60 8.30 1.31e+00 5.83e-01 4.02e+01 angle pdb=" C PHE A 235 " pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " ideal model delta sigma weight residual 111.02 118.18 -7.16 1.61e+00 3.86e-01 1.98e+01 ... (remaining 5033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1924 17.77 - 35.54: 191 35.54 - 53.31: 26 53.31 - 71.07: 4 71.07 - 88.84: 3 Dihedral angle restraints: 2148 sinusoidal: 818 harmonic: 1330 Sorted by residual: dihedral pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU A 292 " pdb=" CG GLU A 292 " pdb=" CD GLU A 292 " pdb=" OE1 GLU A 292 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 447 " pdb=" CD ARG A 447 " pdb=" NE ARG A 447 " pdb=" CZ ARG A 447 " ideal model delta sinusoidal sigma weight residual -90.00 -132.68 42.68 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 2145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 397 0.041 - 0.082: 153 0.082 - 0.123: 32 0.123 - 0.164: 9 0.164 - 0.206: 1 Chirality restraints: 592 Sorted by residual: chirality pdb=" CA PHE A 235 " pdb=" N PHE A 235 " pdb=" C PHE A 235 " pdb=" CB PHE A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 589 not shown) Planarity restraints: 623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " 0.026 2.00e-02 2.50e+03 5.48e-02 3.01e+01 pdb=" C TYR A 233 " -0.095 2.00e-02 2.50e+03 pdb=" O TYR A 233 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 234 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 469 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO A 470 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 235 " 0.023 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE A 235 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 235 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 235 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 235 " 0.006 2.00e-02 2.50e+03 ... (remaining 620 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 638 2.76 - 3.29: 3715 3.29 - 3.83: 6081 3.83 - 4.36: 6485 4.36 - 4.90: 11514 Nonbonded interactions: 28433 Sorted by model distance: nonbonded pdb=" OE1 GLU A 191 " pdb=" OG SER A 255 " model vdw 2.223 3.040 nonbonded pdb=" O VAL A 356 " pdb=" OG SER A 359 " model vdw 2.269 3.040 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.278 3.040 nonbonded pdb=" OE2 GLU A 501 " pdb=" NH1 ARG A 505 " model vdw 2.381 3.120 nonbonded pdb=" O GLU A 223 " pdb=" NZ LYS A 227 " model vdw 2.388 3.120 ... (remaining 28428 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: 0.550 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 0.006 0.144 3697 Z= 0.321 Angle : 0.765 10.358 5038 Z= 0.436 Chirality : 0.045 0.206 592 Planarity : 0.006 0.075 623 Dihedral : 14.110 88.841 1300 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % 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: 1.27 (0.41), residues: 465 helix: 1.14 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.002 0.001 HIS A 139 PHE 0.042 0.002 PHE A 235 TYR 0.011 0.001 TYR A 327 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.12522 ( 281) hydrogen bonds : angle 5.48873 ( 831) covalent geometry : bond 0.00639 ( 3697) covalent geometry : angle 0.76455 ( 5038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.414 Fit side-chains REVERT: A 102 ASP cc_start: 0.6624 (p0) cc_final: 0.6207 (p0) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1009 time to fit residues: 10.3078 Evaluate side-chains 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.223798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.186134 restraints weight = 4384.455| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.15 r_work: 0.4113 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.144 Angle : 0.586 5.743 5038 Z= 0.304 Chirality : 0.043 0.139 592 Planarity : 0.005 0.050 623 Dihedral : 4.265 13.887 507 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.34 % Allowed : 9.90 % Favored : 87.76 % 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: 1.26 (0.41), residues: 465 helix: 1.16 (0.28), residues: 384 sheet: None (None), residues: 0 loop : -0.39 (0.77), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.002 PHE A 164 TYR 0.008 0.001 TYR A 327 ARG 0.001 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 281) hydrogen bonds : angle 4.33925 ( 831) covalent geometry : bond 0.00321 ( 3697) covalent geometry : angle 0.58612 ( 5038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.424 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.1594 time to fit residues: 15.0080 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.224871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187405 restraints weight = 4365.180| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.01 r_work: 0.4110 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3697 Z= 0.137 Angle : 0.582 9.780 5038 Z= 0.294 Chirality : 0.043 0.164 592 Planarity : 0.004 0.039 623 Dihedral : 4.142 12.460 507 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.39 % Allowed : 12.24 % Favored : 84.38 % 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: 1.40 (0.41), residues: 465 helix: 1.27 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.32 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.018 0.002 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.006 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 281) hydrogen bonds : angle 4.17586 ( 831) covalent geometry : bond 0.00312 ( 3697) covalent geometry : angle 0.58218 ( 5038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.373 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.0961 time to fit residues: 9.4674 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** 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 = 0.4601 r_free = 0.4601 target = 0.224878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.186861 restraints weight = 4420.993| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.09 r_work: 0.4102 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.134 Angle : 0.569 6.689 5038 Z= 0.290 Chirality : 0.043 0.155 592 Planarity : 0.004 0.037 623 Dihedral : 4.058 12.401 507 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.39 % Allowed : 14.32 % Favored : 82.29 % 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: 1.55 (0.41), residues: 465 helix: 1.39 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.37 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.016 0.002 PHE A 208 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 281) hydrogen bonds : angle 4.11063 ( 831) covalent geometry : bond 0.00299 ( 3697) covalent geometry : angle 0.56947 ( 5038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.386 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 0.0959 time to fit residues: 9.4690 Evaluate side-chains 71 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** 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 = 0.4602 r_free = 0.4602 target = 0.224217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.185907 restraints weight = 4510.394| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 3.13 r_work: 0.4126 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3697 Z= 0.130 Angle : 0.551 5.329 5038 Z= 0.284 Chirality : 0.043 0.148 592 Planarity : 0.004 0.037 623 Dihedral : 3.999 12.492 507 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.65 % Allowed : 15.36 % Favored : 80.99 % 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: 1.67 (0.41), residues: 465 helix: 1.47 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.33 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.016 0.002 PHE A 208 TYR 0.012 0.001 TYR A 188 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 281) hydrogen bonds : angle 4.04767 ( 831) covalent geometry : bond 0.00294 ( 3697) covalent geometry : angle 0.55057 ( 5038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.379 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 69 average time/residue: 0.1086 time to fit residues: 10.2740 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.225017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.186932 restraints weight = 4499.140| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.13 r_work: 0.4143 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.121 Angle : 0.539 5.322 5038 Z= 0.277 Chirality : 0.042 0.142 592 Planarity : 0.004 0.036 623 Dihedral : 3.941 11.914 507 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.69 % Allowed : 15.36 % Favored : 79.95 % 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: 1.79 (0.41), residues: 465 helix: 1.54 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.21 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.026 0.001 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 281) hydrogen bonds : angle 3.97521 ( 831) covalent geometry : bond 0.00267 ( 3697) covalent geometry : angle 0.53918 ( 5038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.396 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 76 average time/residue: 0.1016 time to fit residues: 10.6640 Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.0050 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.223864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.186428 restraints weight = 4436.661| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 3.12 r_work: 0.4148 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3697 Z= 0.121 Angle : 0.556 5.345 5038 Z= 0.285 Chirality : 0.042 0.167 592 Planarity : 0.004 0.035 623 Dihedral : 3.935 11.870 507 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.17 % Allowed : 15.62 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.41), residues: 465 helix: 1.60 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.17 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.013 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 281) hydrogen bonds : angle 3.94442 ( 831) covalent geometry : bond 0.00264 ( 3697) covalent geometry : angle 0.55586 ( 5038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.390 Fit side-chains REVERT: A 126 LEU cc_start: 0.8643 (mm) cc_final: 0.8305 (mp) outliers start: 16 outliers final: 14 residues processed: 72 average time/residue: 0.1018 time to fit residues: 10.2040 Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.223471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.186028 restraints weight = 4466.768| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 3.11 r_work: 0.4135 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3697 Z= 0.133 Angle : 0.576 5.906 5038 Z= 0.294 Chirality : 0.043 0.148 592 Planarity : 0.004 0.038 623 Dihedral : 3.979 11.807 507 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.43 % Allowed : 15.62 % Favored : 79.95 % 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: 465 helix: 1.61 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.30 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.027 0.002 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 281) hydrogen bonds : angle 4.01585 ( 831) covalent geometry : bond 0.00304 ( 3697) covalent geometry : angle 0.57565 ( 5038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.390 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 68 average time/residue: 0.0991 time to fit residues: 9.3490 Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.224315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.186839 restraints weight = 4380.495| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.08 r_work: 0.4137 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.126 Angle : 0.574 7.373 5038 Z= 0.292 Chirality : 0.043 0.154 592 Planarity : 0.004 0.035 623 Dihedral : 3.963 11.610 507 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.95 % Allowed : 15.89 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.41), residues: 465 helix: 1.64 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.24 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 281) hydrogen bonds : angle 3.98309 ( 831) covalent geometry : bond 0.00280 ( 3697) covalent geometry : angle 0.57356 ( 5038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.394 Fit side-chains REVERT: A 126 LEU cc_start: 0.8536 (mm) cc_final: 0.8199 (mp) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.0966 time to fit residues: 9.6951 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 462 ASN Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.188471 restraints weight = 4422.738| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.07 r_work: 0.4147 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3697 Z= 0.121 Angle : 0.579 8.585 5038 Z= 0.293 Chirality : 0.043 0.174 592 Planarity : 0.004 0.035 623 Dihedral : 3.963 11.647 507 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.91 % Allowed : 16.67 % Favored : 79.43 % 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: 1.94 (0.41), residues: 465 helix: 1.67 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.23 (0.73), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.024 0.001 PHE A 164 TYR 0.013 0.001 TYR A 188 ARG 0.001 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 281) hydrogen bonds : angle 3.95664 ( 831) covalent geometry : bond 0.00256 ( 3697) covalent geometry : angle 0.57863 ( 5038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.395 Fit side-chains REVERT: A 126 LEU cc_start: 0.8504 (mm) cc_final: 0.8184 (mp) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.1027 time to fit residues: 9.5563 Evaluate side-chains 66 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.222102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.185014 restraints weight = 4539.741| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.20 r_work: 0.4130 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.132 Angle : 0.592 8.500 5038 Z= 0.300 Chirality : 0.043 0.173 592 Planarity : 0.004 0.036 623 Dihedral : 3.974 11.594 507 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.65 % Allowed : 16.67 % Favored : 79.69 % 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: 1.90 (0.41), residues: 465 helix: 1.65 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.24 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.025 0.001 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 281) hydrogen bonds : angle 3.99823 ( 831) covalent geometry : bond 0.00300 ( 3697) covalent geometry : angle 0.59222 ( 5038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.11 seconds wall clock time: 34 minutes 46.85 seconds (2086.85 seconds total)