Starting phenix.real_space_refine on Wed Sep 17 03:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrm_61760/09_2025/9jrm_61760.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 2088 2.51 5 N 517 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3090 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'GJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.05, per 1000 atoms: 0.34 Number of scatterers: 3134 At special positions: 0 Unit cell: (68, 67, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 515 8.00 N 517 7.00 C 2088 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: 0.30 Conformation dependent library (CDL) restraints added in 114.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 58 removed outlier: 4.084A pdb=" N GLN A 58 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.050A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.975A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.500A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.527A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.717A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.874A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 264 through 293 removed outlier: 3.511A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 3.905A pdb=" N ALA A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.909A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 418 removed outlier: 3.605A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.556A pdb=" N GLY A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 702 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: 0.48 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.41: 1364 1.41 - 1.59: 1841 1.59 - 1.77: 4 1.77 - 1.95: 16 1.95 - 2.13: 2 Bond restraints: 3227 Sorted by residual: bond pdb=" O9 GJF A 701 " pdb=" P2 GJF A 701 " ideal model delta sigma weight residual 1.602 1.733 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C3 GJF A 701 " pdb=" N8 GJF A 701 " ideal model delta sigma weight residual 1.342 1.448 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.534 1.432 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C14 GJF A 701 " pdb=" N7 GJF A 701 " ideal model delta sigma weight residual 1.336 1.438 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 3222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 4357 4.00 - 8.00: 33 8.00 - 12.00: 12 12.00 - 15.99: 4 15.99 - 19.99: 1 Bond angle restraints: 4407 Sorted by residual: angle pdb=" O3 GJF A 701 " pdb=" P1 GJF A 701 " pdb=" S1 GJF A 701 " ideal model delta sigma weight residual 97.13 117.12 -19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 116.54 101.01 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 98.38 111.04 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C6 GJF A 701 " pdb=" O1 GJF A 701 " pdb=" C7 GJF A 701 " ideal model delta sigma weight residual 110.83 98.67 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" O6 GJF A 701 " ideal model delta sigma weight residual 117.11 104.97 12.14 3.00e+00 1.11e-01 1.64e+01 ... (remaining 4402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 1643 20.96 - 41.91: 198 41.91 - 62.87: 29 62.87 - 83.83: 2 83.83 - 104.78: 7 Dihedral angle restraints: 1879 sinusoidal: 749 harmonic: 1130 Sorted by residual: dihedral pdb=" C9 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sinusoidal sigma weight residual -116.32 -11.54 -104.78 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " pdb=" CZ ARG A 151 " ideal model delta sinusoidal sigma weight residual -90.00 -134.32 44.32 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 1876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 502 0.110 - 0.219: 10 0.219 - 0.329: 1 0.329 - 0.438: 2 0.438 - 0.548: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" P2 GJF A 701 " pdb=" O5 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual True 2.71 3.26 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C16 GJF A 701 " pdb=" C15 GJF A 701 " pdb=" C17 GJF A 701 " pdb=" O8 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C17 GJF A 701 " pdb=" C16 GJF A 701 " pdb=" C18 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.60 2.25 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 513 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 82 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 84 " -0.008 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE A 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 84 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 84 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 84 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 84 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GJF A 701 " -0.012 2.00e-02 2.50e+03 6.80e-03 1.27e+00 pdb=" C11 GJF A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C12 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C13 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C14 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GJF A 701 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GJF A 701 " -0.014 2.00e-02 2.50e+03 pdb=" N4 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" N5 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N6 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GJF A 701 " 0.000 2.00e-02 2.50e+03 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 609 2.76 - 3.30: 3135 3.30 - 3.83: 5568 3.83 - 4.37: 6145 4.37 - 4.90: 10688 Nonbonded interactions: 26145 Sorted by model distance: nonbonded pdb=" O GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.236 3.040 nonbonded pdb=" O HIS A 358 " pdb=" OG SER A 361 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" O VAL A 327 " model vdw 2.358 3.120 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.363 3.040 ... (remaining 26140 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: 1.130 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.120 Find NCS groups from input model: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 3227 Z= 0.350 Angle : 1.013 19.992 4407 Z= 0.424 Chirality : 0.056 0.548 516 Planarity : 0.004 0.043 518 Dihedral : 17.940 104.782 1153 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 27.58 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.44), residues: 378 helix: 1.15 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.61 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 264 TYR 0.011 0.001 TYR A 35 PHE 0.020 0.001 PHE A 84 TRP 0.010 0.001 TRP A 331 HIS 0.001 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00681 ( 3227) covalent geometry : angle 1.01310 ( 4407) hydrogen bonds : bond 0.10651 ( 234) hydrogen bonds : angle 5.39953 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.115 Fit side-chains REVERT: A 66 ASN cc_start: 0.8113 (m110) cc_final: 0.7905 (m110) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0477 time to fit residues: 2.2935 Evaluate side-chains 34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.187431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152370 restraints weight = 3540.347| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.83 r_work: 0.3607 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.159 Angle : 0.579 7.553 4407 Z= 0.283 Chirality : 0.039 0.145 516 Planarity : 0.004 0.045 518 Dihedral : 9.797 78.872 490 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.42 % Allowed : 26.97 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.43), residues: 378 helix: 1.27 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.47 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.012 0.001 TYR A 35 PHE 0.021 0.001 PHE A 84 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3227) covalent geometry : angle 0.57862 ( 4407) hydrogen bonds : bond 0.04000 ( 234) hydrogen bonds : angle 4.15254 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.117 Fit side-chains REVERT: A 76 TYR cc_start: 0.8599 (t80) cc_final: 0.8258 (t80) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.0426 time to fit residues: 2.4527 Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.188274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152919 restraints weight = 3583.309| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.87 r_work: 0.3630 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.138 Angle : 0.535 7.426 4407 Z= 0.268 Chirality : 0.038 0.112 516 Planarity : 0.004 0.044 518 Dihedral : 8.772 76.111 490 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.24 % Allowed : 27.58 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.43), residues: 378 helix: 1.45 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.41 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.011 0.001 TYR A 35 PHE 0.019 0.001 PHE A 84 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3227) covalent geometry : angle 0.53549 ( 4407) hydrogen bonds : bond 0.03825 ( 234) hydrogen bonds : angle 4.02853 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.142 Fit side-chains REVERT: A 40 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: A 89 TYR cc_start: 0.7766 (t80) cc_final: 0.7505 (t80) REVERT: A 266 GLN cc_start: 0.8218 (mm110) cc_final: 0.7999 (mm-40) outliers start: 14 outliers final: 8 residues processed: 46 average time/residue: 0.0401 time to fit residues: 2.6084 Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.190733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153809 restraints weight = 3586.595| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.93 r_work: 0.3626 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.135 Angle : 0.529 7.535 4407 Z= 0.264 Chirality : 0.038 0.113 516 Planarity : 0.004 0.044 518 Dihedral : 8.115 73.519 490 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.45 % Allowed : 26.36 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.44), residues: 378 helix: 1.57 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.42 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.014 0.001 TYR A 287 PHE 0.019 0.001 PHE A 84 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3227) covalent geometry : angle 0.52929 ( 4407) hydrogen bonds : bond 0.03726 ( 234) hydrogen bonds : angle 3.93867 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.126 Fit side-chains REVERT: A 40 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 76 TYR cc_start: 0.8572 (t80) cc_final: 0.8194 (t80) outliers start: 18 outliers final: 13 residues processed: 48 average time/residue: 0.0447 time to fit residues: 3.0059 Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 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 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.185566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150145 restraints weight = 3533.261| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.84 r_work: 0.3610 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.170 Angle : 0.563 7.716 4407 Z= 0.281 Chirality : 0.040 0.117 516 Planarity : 0.004 0.046 518 Dihedral : 8.065 71.677 490 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.06 % Allowed : 25.76 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.44), residues: 378 helix: 1.49 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -1.62 (0.82), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.013 0.001 TYR A 35 PHE 0.022 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3227) covalent geometry : angle 0.56258 ( 4407) hydrogen bonds : bond 0.03935 ( 234) hydrogen bonds : angle 4.01304 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.100 Fit side-chains REVERT: A 40 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: A 89 TYR cc_start: 0.7648 (t80) cc_final: 0.7056 (t80) REVERT: A 130 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7607 (mmm) outliers start: 20 outliers final: 14 residues processed: 50 average time/residue: 0.0389 time to fit residues: 2.7237 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.188400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153223 restraints weight = 3532.846| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.82 r_work: 0.3633 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3227 Z= 0.135 Angle : 0.539 7.701 4407 Z= 0.267 Chirality : 0.038 0.113 516 Planarity : 0.004 0.043 518 Dihedral : 7.811 70.480 490 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.85 % Allowed : 26.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.44), residues: 378 helix: 1.65 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.43 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.011 0.001 TYR A 35 PHE 0.019 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3227) covalent geometry : angle 0.53894 ( 4407) hydrogen bonds : bond 0.03687 ( 234) hydrogen bonds : angle 3.93956 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.114 Fit side-chains REVERT: A 40 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: A 130 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7503 (mmm) outliers start: 16 outliers final: 12 residues processed: 44 average time/residue: 0.0414 time to fit residues: 2.5767 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.186234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150539 restraints weight = 3600.602| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.86 r_work: 0.3605 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.160 Angle : 0.565 7.793 4407 Z= 0.278 Chirality : 0.040 0.147 516 Planarity : 0.004 0.046 518 Dihedral : 7.831 69.841 490 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.45 % Allowed : 26.67 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.43), residues: 378 helix: 1.60 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.45 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.013 0.001 TYR A 35 PHE 0.021 0.001 PHE A 84 TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3227) covalent geometry : angle 0.56493 ( 4407) hydrogen bonds : bond 0.03827 ( 234) hydrogen bonds : angle 3.97542 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.071 Fit side-chains REVERT: A 40 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: A 76 TYR cc_start: 0.8586 (t80) cc_final: 0.8274 (t80) REVERT: A 89 TYR cc_start: 0.7726 (t80) cc_final: 0.7091 (t80) REVERT: A 130 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7629 (mmm) outliers start: 18 outliers final: 14 residues processed: 50 average time/residue: 0.0413 time to fit residues: 2.8919 Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.186878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150963 restraints weight = 3686.869| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.90 r_work: 0.3607 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3227 Z= 0.151 Angle : 0.566 7.785 4407 Z= 0.277 Chirality : 0.040 0.165 516 Planarity : 0.004 0.045 518 Dihedral : 7.759 69.185 490 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.36 % Allowed : 26.06 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.43), residues: 378 helix: 1.63 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.012 0.001 TYR A 35 PHE 0.021 0.001 PHE A 84 TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3227) covalent geometry : angle 0.56555 ( 4407) hydrogen bonds : bond 0.03794 ( 234) hydrogen bonds : angle 3.97309 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.121 Fit side-chains REVERT: A 40 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: A 76 TYR cc_start: 0.8584 (t80) cc_final: 0.8289 (t80) REVERT: A 89 TYR cc_start: 0.7684 (t80) cc_final: 0.7097 (t80) REVERT: A 130 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7648 (mmm) outliers start: 21 outliers final: 15 residues processed: 52 average time/residue: 0.0420 time to fit residues: 3.0553 Evaluate side-chains 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.187288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151616 restraints weight = 3630.059| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.87 r_work: 0.3618 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.142 Angle : 0.561 8.144 4407 Z= 0.274 Chirality : 0.039 0.175 516 Planarity : 0.004 0.044 518 Dihedral : 7.651 68.401 490 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.76 % Allowed : 26.36 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.43), residues: 378 helix: 1.71 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.40 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.012 0.001 TYR A 35 PHE 0.020 0.001 PHE A 84 TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3227) covalent geometry : angle 0.56126 ( 4407) hydrogen bonds : bond 0.03729 ( 234) hydrogen bonds : angle 3.94715 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.109 Fit side-chains REVERT: A 40 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 76 TYR cc_start: 0.8591 (t80) cc_final: 0.8229 (t80) REVERT: A 89 TYR cc_start: 0.7663 (t80) cc_final: 0.7108 (t80) REVERT: A 130 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7638 (mmm) outliers start: 19 outliers final: 16 residues processed: 51 average time/residue: 0.0370 time to fit residues: 2.6694 Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.187361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.151747 restraints weight = 3573.801| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.86 r_work: 0.3611 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.145 Angle : 0.568 8.603 4407 Z= 0.277 Chirality : 0.040 0.170 516 Planarity : 0.004 0.044 518 Dihedral : 7.601 67.651 490 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.76 % Allowed : 26.67 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.43), residues: 378 helix: 1.70 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.48 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.012 0.001 TYR A 35 PHE 0.021 0.001 PHE A 84 TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3227) covalent geometry : angle 0.56831 ( 4407) hydrogen bonds : bond 0.03740 ( 234) hydrogen bonds : angle 3.95717 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.073 Fit side-chains REVERT: A 40 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: A 76 TYR cc_start: 0.8573 (t80) cc_final: 0.8272 (t80) REVERT: A 89 TYR cc_start: 0.7691 (t80) cc_final: 0.7163 (t80) REVERT: A 130 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7650 (mmm) outliers start: 19 outliers final: 17 residues processed: 49 average time/residue: 0.0418 time to fit residues: 2.8650 Evaluate side-chains 55 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.185502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149814 restraints weight = 3604.657| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.86 r_work: 0.3596 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3227 Z= 0.172 Angle : 0.591 8.337 4407 Z= 0.289 Chirality : 0.041 0.164 516 Planarity : 0.004 0.045 518 Dihedral : 7.678 67.154 490 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.45 % Allowed : 27.27 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.43), residues: 378 helix: 1.59 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.57 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.014 0.001 TYR A 35 PHE 0.023 0.001 PHE A 84 TRP 0.012 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3227) covalent geometry : angle 0.59104 ( 4407) hydrogen bonds : bond 0.03903 ( 234) hydrogen bonds : angle 4.02817 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 860.13 seconds wall clock time: 15 minutes 26.35 seconds (926.35 seconds total)