Starting phenix.real_space_refine on Thu Sep 18 23:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.map" model { file = "/net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atw_43835/09_2025/9atw_43835.cif" } resolution = 3.5 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= 0.013 sd= 0.088 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 S 64 5.16 5 C 6720 2.51 5 N 1600 2.21 5 O 1728 1.98 5 H 11840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 21952 Number of models: 1 Model: "" Number of chains: 1 Chain: "AU" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 343 Classifications: {'peptide': 21} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 20} Restraints were copied for chains: AV, AW, AX, AY, AZ, Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax, Ay, Az, A1, A2, A3, A4, A5, A6, A7, A8, A9, A0, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV Time building chain proxies: 1.52, per 1000 atoms: 0.07 Number of scatterers: 21952 At special positions: 0 Unit cell: (69.229, 69.229, 177.278, 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 64 16.00 O 1728 8.00 N 1600 7.00 C 6720 6.00 H 11840 1.00 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: 1.80 Conformation dependent library (CDL) restraints added in 509.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 11840 1.13 - 1.30: 1600 1.30 - 1.47: 2719 1.47 - 1.64: 5665 1.64 - 1.81: 128 Bond restraints: 21952 Sorted by residual: bond pdb=" N GLYAh 2 " pdb=" H GLYAh 2 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N GLYAi 2 " pdb=" H GLYAi 2 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N GLYBE 2 " pdb=" H GLYBE 2 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N GLYBG 2 " pdb=" H GLYBG 2 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N GLYBA 2 " pdb=" H GLYBA 2 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 ... (remaining 21947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 22913 1.32 - 2.64: 11265 2.64 - 3.96: 3236 3.96 - 5.28: 1993 5.28 - 6.60: 1105 Bond angle restraints: 40512 Sorted by residual: angle pdb=" CA PHEAr 18 " pdb=" CB PHEAr 18 " pdb=" CG PHEAr 18 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CA PHEBM 18 " pdb=" CB PHEBM 18 " pdb=" CG PHEBM 18 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CA PHEBA 18 " pdb=" CB PHEBA 18 " pdb=" CG PHEBA 18 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CA PHEA8 18 " pdb=" CB PHEA8 18 " pdb=" CG PHEA8 18 " ideal model delta sigma weight residual 113.80 118.70 -4.90 1.00e+00 1.00e+00 2.40e+01 angle pdb=" CA PHEAy 18 " pdb=" CB PHEAy 18 " pdb=" CG PHEAy 18 " ideal model delta sigma weight residual 113.80 118.70 -4.90 1.00e+00 1.00e+00 2.40e+01 ... (remaining 40507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.43: 7872 12.43 - 24.85: 927 24.85 - 37.28: 481 37.28 - 49.71: 64 49.71 - 62.14: 256 Dihedral angle restraints: 9600 sinusoidal: 5696 harmonic: 3904 Sorted by residual: dihedral pdb=" CA SERAe 13 " pdb=" C SERAe 13 " pdb=" N LEUAe 14 " pdb=" CA LEUAe 14 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SERAm 13 " pdb=" C SERAm 13 " pdb=" N LEUAm 14 " pdb=" CA LEUAm 14 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SERBE 13 " pdb=" C SERBE 13 " pdb=" N LEUBE 14 " pdb=" CA LEUBE 14 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 9597 not shown) Histogram of chiral volume deviations from ideal: 0.011 - 0.063: 768 0.063 - 0.116: 255 0.116 - 0.169: 257 0.169 - 0.221: 256 0.221 - 0.274: 192 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA META7 1 " pdb=" N META7 1 " pdb=" C META7 1 " pdb=" CB META7 1 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA METAV 1 " pdb=" N METAV 1 " pdb=" C METAV 1 " pdb=" CB METAV 1 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA META4 1 " pdb=" N META4 1 " pdb=" C META4 1 " pdb=" CB META4 1 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1725 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYBO 6 " 0.033 2.00e-02 2.50e+03 5.92e-02 3.50e+01 pdb=" N ILEBO 7 " -0.102 2.00e-02 2.50e+03 pdb=" CA ILEBO 7 " 0.029 2.00e-02 2.50e+03 pdb=" H ILEBO 7 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLYBK 6 " 0.032 2.00e-02 2.50e+03 5.92e-02 3.50e+01 pdb=" N ILEBK 7 " -0.102 2.00e-02 2.50e+03 pdb=" CA ILEBK 7 " 0.029 2.00e-02 2.50e+03 pdb=" H ILEBK 7 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLYAZ 6 " -0.032 2.00e-02 2.50e+03 5.91e-02 3.50e+01 pdb=" N ILEAZ 7 " 0.102 2.00e-02 2.50e+03 pdb=" CA ILEAZ 7 " -0.029 2.00e-02 2.50e+03 pdb=" H ILEAZ 7 " -0.041 2.00e-02 2.50e+03 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 5537 2.37 - 2.93: 51256 2.93 - 3.49: 55758 3.49 - 4.04: 79932 4.04 - 4.60: 112682 Nonbonded interactions: 305165 Sorted by model distance: nonbonded pdb="HD12 ILEAz 3 " pdb=" HB3 ALABV 5 " model vdw 1.814 2.440 nonbonded pdb=" HB3 ALAAz 5 " pdb="HD12 ILEBV 3 " model vdw 1.817 2.440 nonbonded pdb="HD12 ILEAy 3 " pdb=" HB3 ALABU 5 " model vdw 1.821 2.440 nonbonded pdb=" HB3 ALAAy 5 " pdb="HD12 ILEBU 3 " model vdw 1.822 2.440 nonbonded pdb="HD12 ILEAx 3 " pdb=" HB3 ALABT 5 " model vdw 1.827 2.440 ... (remaining 305160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'A9' selection = chain 'A0' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' selection = chain 'BJ' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BR' selection = chain 'BS' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' } 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 group one per residue 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: 1.730 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 12.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.012 0.032 10112 Z= 0.676 Angle : 2.181 6.598 13376 Z= 1.413 Chirality : 0.135 0.274 1728 Planarity : 0.009 0.022 1536 Dihedral : 15.033 50.808 3904 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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: -3.62 (0.12), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.10), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.009 PHEA4 18 Details of bonding type rmsd covalent geometry : bond 0.01209 (10112) covalent geometry : angle 2.18062 (13376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AW 1 MET cc_start: 0.5778 (mmt) cc_final: 0.5433 (mmt) REVERT: AX 1 MET cc_start: 0.6004 (mmt) cc_final: 0.5317 (mmt) REVERT: AX 10 VAL cc_start: 0.9178 (t) cc_final: 0.8750 (p) REVERT: AY 1 MET cc_start: 0.5678 (mmt) cc_final: 0.5155 (mmt) REVERT: AZ 1 MET cc_start: 0.5751 (mmt) cc_final: 0.5063 (mmt) REVERT: Ab 10 VAL cc_start: 0.8761 (t) cc_final: 0.8486 (p) REVERT: Ad 10 VAL cc_start: 0.8760 (t) cc_final: 0.8483 (p) REVERT: Ad 13 SER cc_start: 0.8780 (p) cc_final: 0.8546 (p) REVERT: Ae 8 ILE cc_start: 0.7767 (mt) cc_final: 0.7567 (mt) REVERT: Ag 10 VAL cc_start: 0.8517 (t) cc_final: 0.8247 (p) REVERT: Aj 10 VAL cc_start: 0.8501 (t) cc_final: 0.8196 (p) REVERT: Ar 10 VAL cc_start: 0.8435 (t) cc_final: 0.8215 (p) REVERT: A4 1 MET cc_start: 0.6030 (mmt) cc_final: 0.5549 (mmt) REVERT: A5 1 MET cc_start: 0.5843 (mmt) cc_final: 0.5353 (mmt) REVERT: A6 1 MET cc_start: 0.5905 (mmt) cc_final: 0.5344 (mmt) REVERT: A0 13 SER cc_start: 0.8773 (p) cc_final: 0.8534 (p) REVERT: BC 10 VAL cc_start: 0.8554 (t) cc_final: 0.8286 (p) REVERT: BF 10 VAL cc_start: 0.8498 (t) cc_final: 0.8145 (p) REVERT: BH 10 VAL cc_start: 0.8305 (t) cc_final: 0.7995 (p) REVERT: BM 13 SER cc_start: 0.8675 (p) cc_final: 0.8456 (p) REVERT: BO 10 VAL cc_start: 0.8624 (t) cc_final: 0.8396 (p) REVERT: BS 10 VAL cc_start: 0.8906 (t) cc_final: 0.8656 (p) REVERT: BV 14 LEU cc_start: 0.8603 (tt) cc_final: 0.8176 (tt) outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.1430 time to fit residues: 139.8978 Evaluate side-chains 483 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ax 17 GLN BT 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.135178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.103203 restraints weight = 65040.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.107973 restraints weight = 23343.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.110960 restraints weight = 11777.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.112849 restraints weight = 7354.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.114052 restraints weight = 5326.013| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10112 Z= 0.167 Angle : 0.718 5.602 13376 Z= 0.405 Chirality : 0.066 0.163 1728 Planarity : 0.002 0.014 1536 Dihedral : 10.295 21.268 1344 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.71 % Allowed : 18.75 % Favored : 74.54 % 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: -3.43 (0.12), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.09), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.004 PHEBU 18 Details of bonding type rmsd covalent geometry : bond 0.00403 (10112) covalent geometry : angle 0.71786 (13376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 436 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AW 1 MET cc_start: 0.5238 (mmt) cc_final: 0.4744 (mmt) REVERT: AX 1 MET cc_start: 0.5188 (mmt) cc_final: 0.4821 (mmt) REVERT: AY 1 MET cc_start: 0.4992 (mmt) cc_final: 0.4499 (mmt) REVERT: Ak 3 ILE cc_start: 0.8524 (mt) cc_final: 0.8317 (mt) REVERT: A4 1 MET cc_start: 0.5567 (mmt) cc_final: 0.5111 (mmt) REVERT: A5 1 MET cc_start: 0.5329 (mmt) cc_final: 0.4614 (mmt) REVERT: A6 1 MET cc_start: 0.5036 (mmt) cc_final: 0.4525 (mmt) outliers start: 73 outliers final: 57 residues processed: 459 average time/residue: 0.1442 time to fit residues: 109.2965 Evaluate side-chains 464 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 407 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 13 SER Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A8 residue 13 SER Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 15 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain A0 residue 15 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BB residue 15 ILE Chi-restraints excluded: chain BC residue 13 SER Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 13 SER Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.114234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094146 restraints weight = 63956.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.098659 restraints weight = 22482.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.101517 restraints weight = 11081.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.103364 restraints weight = 6816.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.104612 restraints weight = 4906.188| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10112 Z= 0.129 Angle : 0.647 5.352 13376 Z= 0.362 Chirality : 0.064 0.166 1728 Planarity : 0.002 0.013 1536 Dihedral : 8.596 18.874 1344 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 5.51 % Allowed : 23.81 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.17 (0.15), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.11), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00292 (10112) covalent geometry : angle 0.64733 (13376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 421 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.7919 (mm) cc_final: 0.7580 (mp) REVERT: AW 1 MET cc_start: 0.5333 (mmt) cc_final: 0.4807 (mmt) REVERT: AX 1 MET cc_start: 0.5236 (mmt) cc_final: 0.4846 (mmt) REVERT: AY 1 MET cc_start: 0.4860 (mmt) cc_final: 0.4352 (mmt) REVERT: Aa 1 MET cc_start: 0.5177 (mmt) cc_final: 0.4701 (mmt) REVERT: A1 3 ILE cc_start: 0.7938 (mm) cc_final: 0.7612 (mp) REVERT: A4 1 MET cc_start: 0.5584 (mmt) cc_final: 0.5130 (mmt) REVERT: A5 1 MET cc_start: 0.5244 (mmt) cc_final: 0.4664 (mmt) REVERT: A6 1 MET cc_start: 0.5113 (mmt) cc_final: 0.4860 (mmt) REVERT: BT 10 VAL cc_start: 0.8047 (t) cc_final: 0.7763 (p) outliers start: 60 outliers final: 55 residues processed: 447 average time/residue: 0.1585 time to fit residues: 117.5115 Evaluate side-chains 459 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 404 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Ac residue 8 ILE Chi-restraints excluded: chain Ad residue 15 ILE Chi-restraints excluded: chain Ae residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A8 residue 13 SER Chi-restraints excluded: chain A8 residue 14 LEU Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 15 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 14 LEU Chi-restraints excluded: chain BC residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 13 SER Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.096407 restraints weight = 63029.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.101479 restraints weight = 22106.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.104708 restraints weight = 10901.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.106783 restraints weight = 6723.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.108189 restraints weight = 4837.177| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10112 Z= 0.144 Angle : 0.625 4.940 13376 Z= 0.348 Chirality : 0.063 0.164 1728 Planarity : 0.002 0.012 1536 Dihedral : 7.875 18.823 1344 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 7.90 % Allowed : 23.35 % Favored : 68.75 % 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: -3.20 (0.16), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.12), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00323 (10112) covalent geometry : angle 0.62524 (13376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 420 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8084 (mm) cc_final: 0.7811 (mp) REVERT: AW 1 MET cc_start: 0.5218 (mmt) cc_final: 0.4375 (mmt) REVERT: AW 3 ILE cc_start: 0.8402 (mt) cc_final: 0.8118 (mp) REVERT: AX 1 MET cc_start: 0.5107 (mmt) cc_final: 0.4544 (mmt) REVERT: AY 1 MET cc_start: 0.4801 (mmt) cc_final: 0.4316 (mmt) REVERT: A1 3 ILE cc_start: 0.8094 (mm) cc_final: 0.7803 (mp) REVERT: A4 1 MET cc_start: 0.5572 (mmt) cc_final: 0.4879 (mmt) REVERT: A5 1 MET cc_start: 0.4976 (mmt) cc_final: 0.4422 (mmt) REVERT: A6 1 MET cc_start: 0.5031 (mmt) cc_final: 0.4392 (mmt) outliers start: 86 outliers final: 79 residues processed: 463 average time/residue: 0.1535 time to fit residues: 117.0107 Evaluate side-chains 476 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 397 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AW residue 8 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 8 ILE Chi-restraints excluded: chain Aa residue 13 SER Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain At residue 15 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A8 residue 13 SER Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 15 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BC residue 13 SER Chi-restraints excluded: chain BD residue 13 SER Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.109605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.091484 restraints weight = 61199.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.096250 restraints weight = 21047.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.099226 restraints weight = 10014.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.101206 restraints weight = 5962.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.102501 restraints weight = 4104.384| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10112 Z= 0.275 Angle : 0.701 5.292 13376 Z= 0.388 Chirality : 0.061 0.161 1728 Planarity : 0.002 0.010 1536 Dihedral : 8.401 34.157 1344 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 10.39 % Allowed : 25.74 % Favored : 63.88 % 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: -3.51 (0.16), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.12), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHEAZ 18 Details of bonding type rmsd covalent geometry : bond 0.00604 (10112) covalent geometry : angle 0.70135 (13376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 408 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8108 (mm) cc_final: 0.7784 (mp) REVERT: AW 1 MET cc_start: 0.5585 (mmt) cc_final: 0.4536 (mmt) REVERT: AW 3 ILE cc_start: 0.8592 (mt) cc_final: 0.8351 (mp) REVERT: AX 1 MET cc_start: 0.5549 (mmt) cc_final: 0.4627 (mmt) REVERT: AY 1 MET cc_start: 0.5253 (mmt) cc_final: 0.4642 (mmt) REVERT: Aa 10 VAL cc_start: 0.8158 (t) cc_final: 0.7951 (p) REVERT: A1 3 ILE cc_start: 0.8171 (mm) cc_final: 0.7898 (mp) REVERT: A3 1 MET cc_start: 0.5682 (mmt) cc_final: 0.5198 (mmt) REVERT: A4 1 MET cc_start: 0.6062 (mmt) cc_final: 0.5259 (mmt) REVERT: A5 1 MET cc_start: 0.5268 (mmt) cc_final: 0.4598 (mmt) REVERT: A6 10 VAL cc_start: 0.8340 (t) cc_final: 0.8124 (p) REVERT: BA 10 VAL cc_start: 0.8075 (t) cc_final: 0.7855 (p) outliers start: 113 outliers final: 104 residues processed: 471 average time/residue: 0.1729 time to fit residues: 131.5536 Evaluate side-chains 499 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 395 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 8 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 8 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 8 ILE Chi-restraints excluded: chain Aa residue 14 LEU Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ab residue 8 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 8 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 13 SER Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Aw residue 13 SER Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 8 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 8 ILE Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 ILE Chi-restraints excluded: chain A7 residue 14 LEU Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A8 residue 14 LEU Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 15 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain A0 residue 14 LEU Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BQ residue 13 SER Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 15 ILE Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.118366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.100258 restraints weight = 60315.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.105108 restraints weight = 21803.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.108165 restraints weight = 10584.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.110082 restraints weight = 6299.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.111353 restraints weight = 4360.805| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10112 Z= 0.172 Angle : 0.625 4.774 13376 Z= 0.347 Chirality : 0.060 0.164 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.601 26.047 1344 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 10.57 % Allowed : 26.93 % Favored : 62.50 % 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: -3.48 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00386 (10112) covalent geometry : angle 0.62481 (13376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 401 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8134 (mm) cc_final: 0.7828 (mp) REVERT: AW 1 MET cc_start: 0.5674 (mmt) cc_final: 0.4549 (mmt) REVERT: AW 3 ILE cc_start: 0.8554 (mt) cc_final: 0.8330 (mp) REVERT: AW 10 VAL cc_start: 0.8214 (t) cc_final: 0.7931 (p) REVERT: AX 1 MET cc_start: 0.5525 (mmt) cc_final: 0.4593 (mmt) REVERT: AY 1 MET cc_start: 0.5207 (mmt) cc_final: 0.4558 (mmt) REVERT: AZ 3 ILE cc_start: 0.8497 (mt) cc_final: 0.8277 (mt) REVERT: A1 3 ILE cc_start: 0.8169 (mm) cc_final: 0.7892 (mp) REVERT: A3 1 MET cc_start: 0.5645 (mmt) cc_final: 0.5182 (mmt) REVERT: A4 1 MET cc_start: 0.5996 (mmt) cc_final: 0.5134 (mmt) REVERT: A4 3 ILE cc_start: 0.8696 (mt) cc_final: 0.8491 (mt) REVERT: A5 1 MET cc_start: 0.5300 (mmt) cc_final: 0.4599 (mmt) REVERT: A6 10 VAL cc_start: 0.8316 (t) cc_final: 0.8053 (p) REVERT: BA 10 VAL cc_start: 0.8070 (t) cc_final: 0.7842 (p) outliers start: 115 outliers final: 107 residues processed: 470 average time/residue: 0.1717 time to fit residues: 130.6838 Evaluate side-chains 496 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 389 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 8 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 8 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 8 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ab residue 8 ILE Chi-restraints excluded: chain Ac residue 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 14 LEU Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Aw residue 13 SER Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Ay residue 15 ILE Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 13 SER Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 8 ILE Chi-restraints excluded: chain A3 residue 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A8 residue 14 LEU Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 15 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BQ residue 14 LEU Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: An 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.121185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.099838 restraints weight = 61700.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.104799 restraints weight = 22604.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.107950 restraints weight = 11112.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.109938 restraints weight = 6697.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.111244 restraints weight = 4710.117| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10112 Z= 0.134 Angle : 0.604 4.757 13376 Z= 0.334 Chirality : 0.061 0.164 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.143 18.925 1344 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 8.92 % Allowed : 29.60 % Favored : 61.49 % 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: -3.46 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00298 (10112) covalent geometry : angle 0.60437 (13376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 395 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8184 (mm) cc_final: 0.7904 (mp) REVERT: AW 1 MET cc_start: 0.5328 (mmt) cc_final: 0.4193 (mmt) REVERT: AW 3 ILE cc_start: 0.8520 (mt) cc_final: 0.8263 (mp) REVERT: AX 1 MET cc_start: 0.5304 (mmt) cc_final: 0.4378 (mmt) REVERT: AY 1 MET cc_start: 0.4957 (mmt) cc_final: 0.4318 (mmt) REVERT: As 3 ILE cc_start: 0.8565 (mp) cc_final: 0.8356 (mp) REVERT: A1 3 ILE cc_start: 0.8187 (mm) cc_final: 0.7899 (mp) REVERT: A4 1 MET cc_start: 0.5936 (mmt) cc_final: 0.5049 (mmt) REVERT: A5 1 MET cc_start: 0.5130 (mmt) cc_final: 0.4400 (mmt) REVERT: A6 10 VAL cc_start: 0.8381 (t) cc_final: 0.8161 (p) outliers start: 97 outliers final: 93 residues processed: 459 average time/residue: 0.1618 time to fit residues: 120.8494 Evaluate side-chains 478 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 385 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 14 LEU Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 13 SER Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BH residue 15 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BK residue 14 LEU Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 62 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Am 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.116109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.098334 restraints weight = 59646.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.103141 restraints weight = 21211.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.106125 restraints weight = 10169.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.108017 restraints weight = 6035.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.109237 restraints weight = 4174.350| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10112 Z= 0.116 Angle : 0.591 4.742 13376 Z= 0.324 Chirality : 0.061 0.165 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.823 18.070 1344 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 7.90 % Allowed : 30.79 % Favored : 61.31 % 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: -3.44 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00261 (10112) covalent geometry : angle 0.59144 (13376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 396 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8213 (mm) cc_final: 0.7945 (mp) REVERT: AW 1 MET cc_start: 0.5501 (mmt) cc_final: 0.4398 (mmt) REVERT: AW 3 ILE cc_start: 0.8479 (mt) cc_final: 0.8217 (mp) REVERT: AX 1 MET cc_start: 0.5524 (mmt) cc_final: 0.4550 (mmt) REVERT: AX 10 VAL cc_start: 0.8173 (t) cc_final: 0.7929 (p) REVERT: AY 1 MET cc_start: 0.5070 (mmt) cc_final: 0.4462 (mmt) REVERT: A1 3 ILE cc_start: 0.8194 (mm) cc_final: 0.7927 (mp) REVERT: A4 1 MET cc_start: 0.6054 (mmt) cc_final: 0.5270 (mmt) REVERT: A5 1 MET cc_start: 0.5347 (mmt) cc_final: 0.4631 (mmt) REVERT: A6 10 VAL cc_start: 0.8383 (t) cc_final: 0.8133 (p) outliers start: 86 outliers final: 83 residues processed: 456 average time/residue: 0.1555 time to fit residues: 115.2337 Evaluate side-chains 473 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 390 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BJ 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.123150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.101249 restraints weight = 61449.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.106340 restraints weight = 22198.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.109532 restraints weight = 10766.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.111583 restraints weight = 6432.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.112864 restraints weight = 4462.719| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10112 Z= 0.127 Angle : 0.603 5.087 13376 Z= 0.330 Chirality : 0.061 0.168 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.747 18.313 1344 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 7.81 % Allowed : 31.71 % Favored : 60.48 % 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: -3.42 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (10112) covalent geometry : angle 0.60305 (13376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 397 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8217 (mm) cc_final: 0.7933 (mp) REVERT: AW 1 MET cc_start: 0.5333 (mmt) cc_final: 0.4241 (mmt) REVERT: AW 3 ILE cc_start: 0.8481 (mt) cc_final: 0.8216 (mp) REVERT: AX 1 MET cc_start: 0.5484 (mmt) cc_final: 0.4550 (mmt) REVERT: AX 10 VAL cc_start: 0.8052 (t) cc_final: 0.7825 (p) REVERT: AY 1 MET cc_start: 0.5073 (mmt) cc_final: 0.4537 (mmt) REVERT: AZ 3 ILE cc_start: 0.8481 (mt) cc_final: 0.8219 (mt) REVERT: A1 3 ILE cc_start: 0.8227 (mm) cc_final: 0.7958 (mp) REVERT: A4 1 MET cc_start: 0.6024 (mmt) cc_final: 0.5330 (mmt) REVERT: A5 1 MET cc_start: 0.5320 (mmt) cc_final: 0.4640 (mmt) REVERT: A6 10 VAL cc_start: 0.8376 (t) cc_final: 0.8120 (p) outliers start: 85 outliers final: 82 residues processed: 454 average time/residue: 0.1652 time to fit residues: 120.8929 Evaluate side-chains 475 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 393 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Aw residue 13 SER Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BH residue 15 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.122729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.100152 restraints weight = 62460.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.105149 restraints weight = 22800.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.108232 restraints weight = 11287.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.110297 restraints weight = 6959.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.111634 restraints weight = 4923.955| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10112 Z= 0.116 Angle : 0.597 5.144 13376 Z= 0.326 Chirality : 0.061 0.173 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.591 17.644 1344 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.44 % Allowed : 32.44 % Favored : 60.11 % 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: -3.37 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00262 (10112) covalent geometry : angle 0.59673 (13376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 395 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8203 (mm) cc_final: 0.7931 (mp) REVERT: AW 1 MET cc_start: 0.5528 (mmt) cc_final: 0.4639 (mmt) REVERT: AX 1 MET cc_start: 0.5697 (mmt) cc_final: 0.4757 (mmt) REVERT: AY 1 MET cc_start: 0.5317 (mmt) cc_final: 0.4751 (mmt) REVERT: AZ 3 ILE cc_start: 0.8458 (mt) cc_final: 0.8190 (mt) REVERT: A1 3 ILE cc_start: 0.8220 (mm) cc_final: 0.7959 (mp) REVERT: A4 1 MET cc_start: 0.6187 (mmt) cc_final: 0.5520 (mmt) REVERT: A5 1 MET cc_start: 0.5482 (mmt) cc_final: 0.4796 (mmt) REVERT: A6 10 VAL cc_start: 0.8490 (t) cc_final: 0.8232 (p) outliers start: 81 outliers final: 80 residues processed: 450 average time/residue: 0.1745 time to fit residues: 126.6015 Evaluate side-chains 471 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 391 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AX residue 15 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Av residue 15 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 13 SER Chi-restraints excluded: chain BB residue 8 ILE Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 13 SER Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BH residue 15 ILE Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.117796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.099412 restraints weight = 60996.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.104205 restraints weight = 21335.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.107175 restraints weight = 10315.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.109087 restraints weight = 6188.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.110310 restraints weight = 4336.659| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10112 Z= 0.101 Angle : 0.593 5.275 13376 Z= 0.322 Chirality : 0.061 0.169 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.391 17.306 1344 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.89 % Allowed : 33.55 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.31 (0.19), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00232 (10112) covalent geometry : angle 0.59277 (13376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.19 seconds wall clock time: 73 minutes 58.31 seconds (4438.31 seconds total)