Starting phenix.real_space_refine on Fri Jan 24 04:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atw_43835/01_2025/9atw_43835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atw_43835/01_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_43835/01_2025/9atw_43835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atw_43835/01_2025/9atw_43835.map" model { file = "/net/cci-nas-00/data/ceres_data/9atw_43835/01_2025/9atw_43835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atw_43835/01_2025/9atw_43835.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21952 Number of models: 1 Model: "" Number of chains: 1 Chain: "BD" 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: BE, BF, BG, BA, BB, BC, BL, BM, BN, BO, BH, BI, BJ, BK, BT, BU, BV, BP, BQ, BR, BS, A1, A0, A3, A2, A5, A4, A7, A6, A9, A8, AU, AW, AV, AY, AX, AZ, Aa, Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, Ak, Aj, Am, Al, Ao, An, Aq, Ap, As, Ar, Au, At, Aw, Av, Ay, Ax, Az Time building chain proxies: 4.36, per 1000 atoms: 0.20 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: 5.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.55 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: 6.10 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: 0.14 Found NCS groups: ncs_group { reference = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BH' selection = chain 'BI' selection = chain 'BJ' selection = chain 'BK' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BR' selection = chain 'BS' selection = chain 'A1' selection = chain 'A0' selection = chain 'A3' selection = chain 'A2' selection = chain 'A5' selection = chain 'A4' selection = chain 'A7' selection = chain 'A6' selection = chain 'A9' selection = chain 'A8' selection = chain 'AU' selection = chain 'AW' selection = chain 'AV' selection = chain 'AY' selection = chain 'AX' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' selection = chain 'Ae' selection = chain 'Ad' selection = chain 'Ag' selection = chain 'Af' selection = chain 'Ai' selection = chain 'Ah' selection = chain 'Ak' selection = chain 'Aj' selection = chain 'Am' selection = chain 'Al' selection = chain 'Ao' selection = chain 'An' selection = chain 'Aq' selection = chain 'Ap' selection = chain 'As' selection = chain 'Ar' selection = chain 'Au' selection = chain 'At' selection = chain 'Aw' selection = chain 'Av' selection = chain 'Ay' selection = chain 'Ax' selection = chain 'Az' } 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: 1.650 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: 0.360 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 30.740 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 1.849 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AW 1 MET cc_start: 0.5778 (mmt) cc_final: 0.5463 (mmt) REVERT: AX 1 MET cc_start: 0.6004 (mmt) cc_final: 0.5311 (mmt) REVERT: AX 10 VAL cc_start: 0.9178 (t) cc_final: 0.8751 (p) REVERT: AY 1 MET cc_start: 0.5678 (mmt) cc_final: 0.5159 (mmt) REVERT: AZ 1 MET cc_start: 0.5751 (mmt) cc_final: 0.5065 (mmt) REVERT: Ab 8 ILE cc_start: 0.7822 (mt) cc_final: 0.7590 (mt) REVERT: Ab 10 VAL cc_start: 0.8761 (t) cc_final: 0.8483 (p) REVERT: Ad 10 VAL cc_start: 0.8760 (t) cc_final: 0.8480 (p) REVERT: Ad 13 SER cc_start: 0.8780 (p) cc_final: 0.8545 (p) REVERT: Ag 10 VAL cc_start: 0.8517 (t) cc_final: 0.8204 (p) REVERT: Aj 10 VAL cc_start: 0.8501 (t) cc_final: 0.8199 (p) REVERT: Ar 10 VAL cc_start: 0.8435 (t) cc_final: 0.8192 (p) REVERT: A4 1 MET cc_start: 0.6030 (mmt) cc_final: 0.5550 (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: 0.8140 (p) REVERT: BH 10 VAL cc_start: 0.8305 (t) cc_final: 0.7990 (p) REVERT: BM 13 SER cc_start: 0.8675 (p) cc_final: 0.8460 (p) REVERT: BO 10 VAL cc_start: 0.8624 (t) cc_final: 0.8395 (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: 0.8175 (tt) outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.3381 time to fit residues: 322.2131 Evaluate side-chains 482 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.105931 restraints weight = 64834.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.110584 restraints weight = 22831.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.113556 restraints weight = 11380.974| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4234 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= 0.158 Angle : 0.717 5.683 13376 Z= 0.405 Chirality : 0.066 0.164 1728 Planarity : 0.002 0.014 1536 Dihedral : 10.483 21.438 1344 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.71 % Allowed : 19.21 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.12), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.09), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHEBP 18 *********************** 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 513 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 440 time to evaluate : 1.816 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: AW 1 MET cc_start: 0.5150 (mmt) cc_final: 0.4549 (mmt) REVERT: AX 1 MET cc_start: 0.5057 (mmt) cc_final: 0.4559 (mmt) REVERT: AY 1 MET cc_start: 0.4881 (mmt) cc_final: 0.4392 (mmt) REVERT: A1 1 MET cc_start: 0.6730 (mmt) cc_final: 0.6181 (mmt) REVERT: A4 1 MET cc_start: 0.5435 (mmt) cc_final: 0.4992 (mmt) REVERT: A5 1 MET cc_start: 0.5151 (mmt) cc_final: 0.4406 (mmt) REVERT: A6 1 MET cc_start: 0.4950 (mmt) cc_final: 0.4405 (mmt) REVERT: BF 13 SER cc_start: 0.9003 (p) cc_final: 0.8724 (m) outliers start: 73 outliers final: 56 residues processed: 461 average time/residue: 0.3500 time to fit residues: 261.5711 Evaluate side-chains 457 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 401 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 8 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 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 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 84 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.111070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.092995 restraints weight = 61650.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.097616 restraints weight = 20813.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.100542 restraints weight = 9929.102| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10112 Z= 0.260 Angle : 0.725 5.035 13376 Z= 0.403 Chirality : 0.063 0.169 1728 Planarity : 0.002 0.013 1536 Dihedral : 9.201 24.137 1344 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 8.82 % Allowed : 20.59 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.14), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.11), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHEAw 18 *********************** 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 522 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 426 time to evaluate : 1.932 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: AU 1 MET cc_start: 0.6472 (mmt) cc_final: 0.5863 (mmt) REVERT: AU 3 ILE cc_start: 0.8061 (mm) cc_final: 0.7807 (mp) REVERT: AV 10 VAL cc_start: 0.8440 (t) cc_final: 0.8185 (t) REVERT: AW 1 MET cc_start: 0.5228 (mmt) cc_final: 0.4612 (mmt) REVERT: AX 1 MET cc_start: 0.5276 (mmt) cc_final: 0.4498 (mmt) REVERT: AY 1 MET cc_start: 0.4779 (mmt) cc_final: 0.4291 (mmt) REVERT: Ad 10 VAL cc_start: 0.8262 (t) cc_final: 0.7976 (p) REVERT: A1 1 MET cc_start: 0.6666 (mmt) cc_final: 0.6008 (mmt) REVERT: A1 3 ILE cc_start: 0.8015 (mm) cc_final: 0.7684 (mp) REVERT: A2 1 MET cc_start: 0.5697 (mmt) cc_final: 0.5458 (mmt) REVERT: A4 1 MET cc_start: 0.5565 (mmt) cc_final: 0.4882 (mmt) REVERT: A5 1 MET cc_start: 0.5075 (mmt) cc_final: 0.4510 (mmt) REVERT: A6 10 VAL cc_start: 0.8405 (t) cc_final: 0.8113 (p) REVERT: BA 10 VAL cc_start: 0.8183 (t) cc_final: 0.7916 (p) outliers start: 96 outliers final: 93 residues processed: 465 average time/residue: 0.3677 time to fit residues: 273.6678 Evaluate side-chains 497 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 404 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 8 ILE Chi-restraints excluded: chain AX residue 4 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 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 Ae residue 13 SER Chi-restraints excluded: chain Ae residue 14 LEU 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 As residue 4 ILE Chi-restraints excluded: chain As residue 8 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 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 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 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 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 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A6 residue 15 ILE Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 14 LEU Chi-restraints excluded: chain A8 residue 4 ILE 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 A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BA residue 14 LEU Chi-restraints excluded: chain BB residue 15 ILE Chi-restraints excluded: chain BC residue 13 SER Chi-restraints excluded: chain BD residue 13 SER Chi-restraints excluded: chain BD residue 15 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 BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE 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 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 BS residue 14 LEU 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 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 69 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.117976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.097123 restraints weight = 62445.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.102023 restraints weight = 21751.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.105173 restraints weight = 10609.515| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10112 Z= 0.187 Angle : 0.641 4.951 13376 Z= 0.359 Chirality : 0.062 0.163 1728 Planarity : 0.002 0.011 1536 Dihedral : 8.187 23.966 1344 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 9.19 % Allowed : 26.29 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.12), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHEAw 18 *********************** 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 508 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 408 time to evaluate : 1.752 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: AU 1 MET cc_start: 0.6432 (mmt) cc_final: 0.5745 (mmt) REVERT: AU 3 ILE cc_start: 0.8134 (mm) cc_final: 0.7846 (mp) REVERT: AW 1 MET cc_start: 0.5326 (mmt) cc_final: 0.4442 (mmt) REVERT: AW 3 ILE cc_start: 0.8512 (mt) cc_final: 0.8261 (mp) REVERT: AX 1 MET cc_start: 0.5235 (mmt) cc_final: 0.4415 (mmt) REVERT: AY 1 MET cc_start: 0.4893 (mmt) cc_final: 0.4318 (mmt) REVERT: Aa 10 VAL cc_start: 0.8267 (t) cc_final: 0.8043 (p) REVERT: Ad 10 VAL cc_start: 0.8362 (t) cc_final: 0.8014 (p) REVERT: A1 1 MET cc_start: 0.6754 (mmt) cc_final: 0.6088 (mmt) REVERT: A1 3 ILE cc_start: 0.8092 (mm) cc_final: 0.7846 (mp) REVERT: A1 16 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A2 1 MET cc_start: 0.5554 (mmt) cc_final: 0.5284 (mmt) REVERT: A4 1 MET cc_start: 0.5637 (mmt) cc_final: 0.4771 (mmt) REVERT: A5 1 MET cc_start: 0.5033 (mmt) cc_final: 0.4463 (mmt) REVERT: A6 10 VAL cc_start: 0.8341 (t) cc_final: 0.8043 (p) outliers start: 100 outliers final: 91 residues processed: 460 average time/residue: 0.3753 time to fit residues: 278.3432 Evaluate side-chains 483 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 392 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 Ab residue 8 ILE Chi-restraints excluded: chain Ac residue 3 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 Ai residue 15 ILE Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Ak residue 8 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 Ao residue 14 LEU 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 8 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 4 ILE 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 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 A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A4 residue 4 ILE 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 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A8 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 14 LEU 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 BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER 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 BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE 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 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 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.113760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.093427 restraints weight = 62830.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.098019 restraints weight = 22554.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.100977 restraints weight = 11131.204| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10112 Z= 0.129 Angle : 0.601 4.869 13376 Z= 0.335 Chirality : 0.061 0.159 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.498 18.369 1344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 8.73 % Allowed : 27.48 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 *********************** 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 501 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 406 time to evaluate : 1.776 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: AU 1 MET cc_start: 0.6447 (mmt) cc_final: 0.5842 (mmt) REVERT: AU 3 ILE cc_start: 0.8123 (mm) cc_final: 0.7843 (mp) REVERT: AW 1 MET cc_start: 0.5225 (mmt) cc_final: 0.4219 (mmt) REVERT: AW 3 ILE cc_start: 0.8510 (mt) cc_final: 0.8239 (mp) REVERT: AX 1 MET cc_start: 0.5150 (mmt) cc_final: 0.4270 (mmt) REVERT: AY 1 MET cc_start: 0.4739 (mmt) cc_final: 0.4127 (mmt) REVERT: Aa 10 VAL cc_start: 0.8196 (t) cc_final: 0.7975 (p) REVERT: A1 1 MET cc_start: 0.6642 (mmt) cc_final: 0.5930 (mmt) REVERT: A1 3 ILE cc_start: 0.8164 (mm) cc_final: 0.7847 (mp) REVERT: A2 1 MET cc_start: 0.5419 (mmt) cc_final: 0.5139 (mmt) REVERT: A4 1 MET cc_start: 0.5684 (mmt) cc_final: 0.4779 (mmt) REVERT: A5 1 MET cc_start: 0.4916 (mmt) cc_final: 0.4241 (mmt) REVERT: A6 10 VAL cc_start: 0.8280 (t) cc_final: 0.7964 (p) outliers start: 95 outliers final: 88 residues processed: 460 average time/residue: 0.3603 time to fit residues: 266.0695 Evaluate side-chains 476 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 388 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AY 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 Aa residue 8 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 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 Ai residue 13 SER Chi-restraints excluded: chain Ak residue 8 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 Ao residue 14 LEU 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 8 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 13 SER 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 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 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 A7 residue 4 ILE Chi-restraints excluded: chain A8 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 14 LEU 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 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.123926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.101671 restraints weight = 61361.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.106701 restraints weight = 22500.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.109899 restraints weight = 11128.265| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10112 Z= 0.195 Angle : 0.632 4.715 13376 Z= 0.350 Chirality : 0.060 0.151 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.587 25.243 1344 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 10.20 % Allowed : 27.11 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAY 18 *********************** 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 507 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 396 time to evaluate : 1.829 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: AU 1 MET cc_start: 0.6444 (mmt) cc_final: 0.5950 (mmt) REVERT: AU 3 ILE cc_start: 0.8129 (mm) cc_final: 0.7774 (mp) REVERT: AW 1 MET cc_start: 0.5319 (mmt) cc_final: 0.4201 (mmt) REVERT: AW 3 ILE cc_start: 0.8585 (mt) cc_final: 0.8338 (mp) REVERT: AX 1 MET cc_start: 0.5321 (mmt) cc_final: 0.4442 (mmt) REVERT: AY 1 MET cc_start: 0.4821 (mmt) cc_final: 0.4193 (mmt) REVERT: Ay 10 VAL cc_start: 0.7945 (t) cc_final: 0.7713 (p) REVERT: A1 1 MET cc_start: 0.6656 (mmt) cc_final: 0.6267 (mmt) REVERT: A1 3 ILE cc_start: 0.8139 (mm) cc_final: 0.7826 (mp) REVERT: A2 1 MET cc_start: 0.5321 (mmt) cc_final: 0.5117 (mmt) REVERT: A4 1 MET cc_start: 0.5725 (mmt) cc_final: 0.4800 (mmt) REVERT: A5 1 MET cc_start: 0.5048 (mmt) cc_final: 0.4293 (mmt) REVERT: A6 10 VAL cc_start: 0.8323 (t) cc_final: 0.8027 (p) REVERT: BA 10 VAL cc_start: 0.7987 (t) cc_final: 0.7751 (p) REVERT: BL 3 ILE cc_start: 0.8582 (mt) cc_final: 0.8362 (mt) outliers start: 111 outliers final: 105 residues processed: 461 average time/residue: 0.3797 time to fit residues: 277.7912 Evaluate side-chains 493 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 388 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 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 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 8 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 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 8 ILE 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 8 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 14 LEU 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 3 ILE 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 A2 residue 13 SER 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 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 A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A8 residue 4 ILE 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 14 LEU 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 BD residue 15 ILE 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 BK residue 14 LEU Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 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 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 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 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.121872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.099874 restraints weight = 62062.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.104836 restraints weight = 22441.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.107987 restraints weight = 11091.108| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10112 Z= 0.193 Angle : 0.627 4.552 13376 Z= 0.346 Chirality : 0.060 0.157 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.437 26.895 1344 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 10.20 % Allowed : 28.22 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAX 18 *********************** 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 499 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 388 time to evaluate : 1.743 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: AU 1 MET cc_start: 0.6365 (mmt) cc_final: 0.6047 (mmt) REVERT: AU 3 ILE cc_start: 0.8169 (mm) cc_final: 0.7809 (mp) REVERT: AW 1 MET cc_start: 0.5090 (mmt) cc_final: 0.3979 (mmt) REVERT: AW 3 ILE cc_start: 0.8578 (mt) cc_final: 0.8320 (mp) REVERT: AW 10 VAL cc_start: 0.8045 (t) cc_final: 0.7772 (p) REVERT: AX 1 MET cc_start: 0.5303 (mmt) cc_final: 0.4432 (mmt) REVERT: AY 1 MET cc_start: 0.4900 (mmt) cc_final: 0.4284 (mmt) REVERT: A1 1 MET cc_start: 0.6623 (mmt) cc_final: 0.6358 (mmt) REVERT: A1 3 ILE cc_start: 0.8160 (mm) cc_final: 0.7855 (mp) REVERT: A4 1 MET cc_start: 0.5729 (mmt) cc_final: 0.4979 (mmt) REVERT: A5 1 MET cc_start: 0.5076 (mmt) cc_final: 0.4415 (mmt) REVERT: A6 10 VAL cc_start: 0.8324 (t) cc_final: 0.8006 (p) REVERT: BA 10 VAL cc_start: 0.7978 (t) cc_final: 0.7769 (p) REVERT: BL 3 ILE cc_start: 0.8614 (mt) cc_final: 0.8394 (mt) outliers start: 111 outliers final: 106 residues processed: 462 average time/residue: 0.3861 time to fit residues: 280.2648 Evaluate side-chains 488 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 382 time to evaluate : 1.925 ------------------------------------------------------------------------------- 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 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 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 8 ILE Chi-restraints excluded: chain Aa residue 14 LEU 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 Ad residue 14 LEU 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 Ak residue 8 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 8 ILE 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 8 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 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 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 A5 residue 14 LEU Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER 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 14 LEU 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 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 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 BP residue 13 SER Chi-restraints excluded: chain BP residue 14 LEU 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 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 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 75 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4422 r_free = 0.4422 target = 0.124507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.102292 restraints weight = 61053.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.107391 restraints weight = 22110.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.110620 restraints weight = 10793.464| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10112 Z= 0.102 Angle : 0.587 4.360 13376 Z= 0.321 Chirality : 0.061 0.166 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.797 18.310 1344 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.54 % Allowed : 31.43 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHEAy 18 *********************** 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 480 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 398 time to evaluate : 1.760 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 1 MET cc_start: 0.6324 (mmt) cc_final: 0.5973 (mmt) REVERT: AU 3 ILE cc_start: 0.8184 (mm) cc_final: 0.7879 (mp) REVERT: AW 1 MET cc_start: 0.5062 (mmt) cc_final: 0.3994 (mmt) REVERT: AW 3 ILE cc_start: 0.8438 (mt) cc_final: 0.8176 (mp) REVERT: AW 10 VAL cc_start: 0.8210 (t) cc_final: 0.7875 (p) REVERT: AX 1 MET cc_start: 0.5316 (mmt) cc_final: 0.4432 (mmt) REVERT: AY 1 MET cc_start: 0.4789 (mmt) cc_final: 0.4198 (mmt) REVERT: AZ 3 ILE cc_start: 0.8483 (mt) cc_final: 0.8242 (mt) REVERT: A1 3 ILE cc_start: 0.8222 (mm) cc_final: 0.7948 (mp) REVERT: A4 1 MET cc_start: 0.5440 (mmt) cc_final: 0.4740 (mmt) REVERT: A5 1 MET cc_start: 0.5177 (mmt) cc_final: 0.4520 (mmt) REVERT: A6 10 VAL cc_start: 0.8312 (t) cc_final: 0.7756 (p) outliers start: 82 outliers final: 76 residues processed: 459 average time/residue: 0.3859 time to fit residues: 282.7171 Evaluate side-chains 463 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 387 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 AY 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 Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ak residue 8 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE 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 8 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 Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER 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 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 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 A6 residue 13 SER 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 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER 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 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 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 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 3 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BU 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.125761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.102637 restraints weight = 62183.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.107498 restraints weight = 23451.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.110565 restraints weight = 11851.287| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10112 Z= 0.167 Angle : 0.619 4.159 13376 Z= 0.339 Chirality : 0.060 0.165 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.913 20.649 1344 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 7.90 % Allowed : 31.71 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAU 18 *********************** 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 473 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 387 time to evaluate : 1.870 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: AU 1 MET cc_start: 0.6231 (mmt) cc_final: 0.6001 (mmt) REVERT: AU 3 ILE cc_start: 0.8145 (mm) cc_final: 0.7825 (mp) REVERT: AW 1 MET cc_start: 0.5039 (mmt) cc_final: 0.3946 (mmt) REVERT: AW 3 ILE cc_start: 0.8488 (mt) cc_final: 0.8219 (mp) REVERT: AX 1 MET cc_start: 0.5282 (mmt) cc_final: 0.4402 (mmt) REVERT: AY 1 MET cc_start: 0.4932 (mmt) cc_final: 0.4416 (mmt) REVERT: AZ 3 ILE cc_start: 0.8565 (mt) cc_final: 0.8322 (mt) REVERT: A1 3 ILE cc_start: 0.8190 (mm) cc_final: 0.7877 (mp) REVERT: A4 1 MET cc_start: 0.5590 (mmt) cc_final: 0.5014 (mmt) REVERT: A5 1 MET cc_start: 0.5098 (mmt) cc_final: 0.4466 (mmt) REVERT: A6 10 VAL cc_start: 0.8235 (t) cc_final: 0.7903 (p) REVERT: BL 3 ILE cc_start: 0.8602 (mt) cc_final: 0.8380 (mt) outliers start: 86 outliers final: 84 residues processed: 453 average time/residue: 0.3966 time to fit residues: 283.1900 Evaluate side-chains 467 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 383 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 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 14 LEU 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 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 8 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE Chi-restraints excluded: chain Ap residue 14 LEU 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 8 ILE Chi-restraints excluded: chain At residue 3 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 8 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 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 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 A6 residue 13 SER 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 BB residue 8 ILE Chi-restraints excluded: chain BD residue 3 ILE 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 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 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 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 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 88 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.126321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.102584 restraints weight = 62151.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.107603 restraints weight = 22693.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.110733 restraints weight = 11244.076| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.7182 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= 0.143 Angle : 0.605 4.341 13376 Z= 0.331 Chirality : 0.060 0.163 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.808 20.362 1344 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.35 % Allowed : 32.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (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 0.005 0.001 PHEAy 18 ********************** 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 462 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 382 time to evaluate : 1.875 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: AU 1 MET cc_start: 0.6424 (mmt) cc_final: 0.6215 (mmt) REVERT: AU 3 ILE cc_start: 0.8137 (mm) cc_final: 0.7816 (mp) REVERT: AW 1 MET cc_start: 0.5224 (mmt) cc_final: 0.4303 (mmt) REVERT: AX 1 MET cc_start: 0.5494 (mmt) cc_final: 0.4628 (mmt) REVERT: AY 1 MET cc_start: 0.5079 (mmt) cc_final: 0.4552 (mmt) REVERT: AZ 3 ILE cc_start: 0.8557 (mt) cc_final: 0.8305 (mt) REVERT: A1 3 ILE cc_start: 0.8123 (mm) cc_final: 0.7824 (mp) REVERT: A4 1 MET cc_start: 0.5747 (mmt) cc_final: 0.5189 (mmt) REVERT: A5 1 MET cc_start: 0.5221 (mmt) cc_final: 0.4568 (mmt) REVERT: A6 10 VAL cc_start: 0.8393 (t) cc_final: 0.8128 (p) REVERT: BL 3 ILE cc_start: 0.8575 (mt) cc_final: 0.8350 (mt) outliers start: 80 outliers final: 77 residues processed: 445 average time/residue: 0.3974 time to fit residues: 280.6382 Evaluate side-chains 460 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 383 time to evaluate : 1.969 ------------------------------------------------------------------------------- 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 AY 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 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 8 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE Chi-restraints excluded: chain Ap residue 14 LEU 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 8 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 Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER 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 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 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 13 SER 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 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER 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 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 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 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 30 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.115226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.096802 restraints weight = 62145.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.101529 restraints weight = 21609.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.104469 restraints weight = 10412.866| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10112 Z= 0.162 Angle : 0.617 4.347 13376 Z= 0.337 Chirality : 0.060 0.162 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.856 23.035 1344 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 8.18 % Allowed : 31.25 % Favored : 60.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAU 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7876.98 seconds wall clock time: 140 minutes 20.63 seconds (8420.63 seconds total)