Starting phenix.real_space_refine on Wed Jun 18 13:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atw_43835/06_2025/9atw_43835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atw_43835/06_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_43835/06_2025/9atw_43835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atw_43835/06_2025/9atw_43835.map" model { file = "/net/cci-nas-00/data/ceres_data/9atw_43835/06_2025/9atw_43835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atw_43835/06_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-5710/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: 4.84, per 1000 atoms: 0.22 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: 5.48 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: 2.95 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: 6.63 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: 2.220 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: 0.350 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 33.930 Find NCS groups from input model: 0.400 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd covalent geometry : bond 0.01209 (10112) covalent geometry : angle 2.18062 (13376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 1.830 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: 0.3297 time to fit residues: 313.7893 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 = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.105952 restraints weight = 64834.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.110596 restraints weight = 22807.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.113566 restraints weight = 11371.884| |-----------------------------------------------------------------------------| 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 Details of bonding type rmsd covalent geometry : bond 0.00382 (10112) covalent geometry : angle 0.71692 (13376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 440 time to evaluate : 2.554 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: 0.5153 (mmt) cc_final: 0.4552 (mmt) REVERT: AX 1 MET cc_start: 0.5061 (mmt) cc_final: 0.4563 (mmt) REVERT: AY 1 MET cc_start: 0.4883 (mmt) cc_final: 0.4394 (mmt) REVERT: A1 1 MET cc_start: 0.6732 (mmt) cc_final: 0.6183 (mmt) REVERT: A4 1 MET cc_start: 0.5439 (mmt) cc_final: 0.4995 (mmt) REVERT: A5 1 MET cc_start: 0.5155 (mmt) cc_final: 0.4408 (mmt) REVERT: A6 1 MET cc_start: 0.4955 (mmt) cc_final: 0.4410 (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: 0.4308 time to fit residues: 322.8361 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 : 3.194 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 6.9990 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 = 0.4297 r_free = 0.4297 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.092942 restraints weight = 61588.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.097579 restraints weight = 20710.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.100513 restraints weight = 9875.809| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10112 Z= 0.252 Angle : 0.724 5.019 13376 Z= 0.403 Chirality : 0.064 0.171 1728 Planarity : 0.002 0.013 1536 Dihedral : 9.202 24.897 1344 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 8.82 % Allowed : 20.68 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.54 (0.14), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.11), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00561 (10112) covalent geometry : angle 0.72368 (13376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 428 time to evaluate : 1.943 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: 0.6399 (mmt) cc_final: 0.5808 (mmt) REVERT: AU 3 ILE cc_start: 0.8048 (mm) cc_final: 0.7796 (mp) REVERT: AV 10 VAL cc_start: 0.8421 (t) cc_final: 0.8161 (t) REVERT: AW 1 MET cc_start: 0.5173 (mmt) cc_final: 0.4563 (mmt) REVERT: AX 1 MET cc_start: 0.5223 (mmt) cc_final: 0.4457 (mmt) REVERT: AY 1 MET cc_start: 0.4735 (mmt) cc_final: 0.4250 (mmt) REVERT: Ad 10 VAL cc_start: 0.8232 (t) cc_final: 0.7947 (p) REVERT: A1 1 MET cc_start: 0.6630 (mmt) cc_final: 0.6058 (mmt) REVERT: A1 3 ILE cc_start: 0.8050 (mm) cc_final: 0.7779 (mp) REVERT: A4 1 MET cc_start: 0.5515 (mmt) cc_final: 0.4840 (mmt) REVERT: A5 1 MET cc_start: 0.5048 (mmt) cc_final: 0.4480 (mmt) REVERT: A6 10 VAL cc_start: 0.8384 (t) cc_final: 0.8102 (p) REVERT: BA 10 VAL cc_start: 0.8156 (t) cc_final: 0.7912 (p) outliers start: 96 outliers final: 92 residues processed: 467 average time/residue: 0.3596 time to fit residues: 267.6229 Evaluate side-chains 498 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 406 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 Ab residue 14 LEU 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 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 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: 5.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.110957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.092719 restraints weight = 62114.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.097419 restraints weight = 21478.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.100395 restraints weight = 10367.821| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10112 Z= 0.160 Angle : 0.633 5.000 13376 Z= 0.353 Chirality : 0.062 0.164 1728 Planarity : 0.002 0.011 1536 Dihedral : 8.059 21.244 1344 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 9.10 % Allowed : 26.38 % 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: -3.39 (0.16), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.12), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHEAw 18 Details of bonding type rmsd covalent geometry : bond 0.00359 (10112) covalent geometry : angle 0.63278 (13376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 409 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 1 MET cc_start: 0.6370 (mmt) cc_final: 0.5705 (mmt) REVERT: AU 3 ILE cc_start: 0.8132 (mm) cc_final: 0.7839 (mp) REVERT: AW 1 MET cc_start: 0.5196 (mmt) cc_final: 0.4334 (mmt) REVERT: AW 3 ILE cc_start: 0.8515 (mt) cc_final: 0.8260 (mp) REVERT: AX 1 MET cc_start: 0.5110 (mmt) cc_final: 0.4304 (mmt) REVERT: AY 1 MET cc_start: 0.4644 (mmt) cc_final: 0.4097 (mmt) REVERT: Aa 10 VAL cc_start: 0.8192 (t) cc_final: 0.7963 (p) REVERT: A1 1 MET cc_start: 0.6699 (mmt) cc_final: 0.6042 (mmt) REVERT: A1 3 ILE cc_start: 0.8110 (mm) cc_final: 0.7838 (mp) REVERT: A2 15 ILE cc_start: 0.8610 (mt) cc_final: 0.8340 (pt) REVERT: A4 1 MET cc_start: 0.5532 (mmt) cc_final: 0.4691 (mmt) REVERT: A5 1 MET cc_start: 0.4889 (mmt) cc_final: 0.4310 (mmt) REVERT: A6 10 VAL cc_start: 0.8270 (t) cc_final: 0.7960 (p) outliers start: 99 outliers final: 91 residues processed: 457 average time/residue: 0.3647 time to fit residues: 266.6200 Evaluate side-chains 486 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 395 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 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 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 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 13 SER Chi-restraints excluded: chain Ai residue 15 ILE Chi-restraints excluded: chain Aj residue 14 LEU 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 A3 residue 15 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 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 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 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 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: 6.9990 chunk 14 optimal weight: 0.0070 chunk 85 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.121140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.102880 restraints weight = 59615.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.107801 restraints weight = 21349.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.110826 restraints weight = 10357.152| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10112 Z= 0.121 Angle : 0.596 4.765 13376 Z= 0.331 Chirality : 0.062 0.159 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.380 18.128 1344 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 8.18 % Allowed : 28.12 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00282 (10112) covalent geometry : angle 0.59646 (13376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 404 time to evaluate : 1.756 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: AU 1 MET cc_start: 0.6464 (mmt) cc_final: 0.5907 (mmt) REVERT: AU 3 ILE cc_start: 0.8135 (mm) cc_final: 0.7857 (mp) REVERT: AW 1 MET cc_start: 0.5230 (mmt) cc_final: 0.4283 (mmt) REVERT: AW 3 ILE cc_start: 0.8481 (mt) cc_final: 0.8210 (mp) REVERT: AX 1 MET cc_start: 0.5150 (mmt) cc_final: 0.4329 (mmt) REVERT: AY 1 MET cc_start: 0.4719 (mmt) cc_final: 0.4117 (mmt) REVERT: Aa 10 VAL cc_start: 0.8115 (t) cc_final: 0.7865 (p) REVERT: A1 1 MET cc_start: 0.6600 (mmt) cc_final: 0.5851 (mmt) REVERT: A1 3 ILE cc_start: 0.8150 (mm) cc_final: 0.7835 (mp) REVERT: A4 1 MET cc_start: 0.5673 (mmt) cc_final: 0.4786 (mmt) REVERT: A5 1 MET cc_start: 0.4922 (mmt) cc_final: 0.4260 (mmt) REVERT: A6 10 VAL cc_start: 0.8237 (t) cc_final: 0.7915 (p) outliers start: 89 outliers final: 82 residues processed: 453 average time/residue: 0.3482 time to fit residues: 253.9374 Evaluate side-chains 475 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 393 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 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 Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain 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 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 A3 residue 15 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 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: 6.9990 chunk 124 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.124700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.101930 restraints weight = 61922.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.106858 restraints weight = 22756.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.110037 restraints weight = 11363.350| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10112 Z= 0.290 Angle : 0.699 4.606 13376 Z= 0.386 Chirality : 0.060 0.152 1728 Planarity : 0.002 0.009 1536 Dihedral : 8.182 35.731 1344 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 11.03 % Allowed : 26.29 % 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: -3.57 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHEAY 18 Details of bonding type rmsd covalent geometry : bond 0.00641 (10112) covalent geometry : angle 0.69916 (13376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 389 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 1 MET cc_start: 0.6479 (mmt) cc_final: 0.6103 (mmt) REVERT: AU 3 ILE cc_start: 0.8068 (mm) cc_final: 0.7721 (mp) REVERT: AW 1 MET cc_start: 0.5334 (mmt) cc_final: 0.4255 (mmt) REVERT: AW 3 ILE cc_start: 0.8626 (mt) cc_final: 0.8376 (mp) REVERT: AW 10 VAL cc_start: 0.7997 (t) cc_final: 0.7681 (p) REVERT: AX 1 MET cc_start: 0.5482 (mmt) cc_final: 0.4609 (mmt) REVERT: AX 10 VAL cc_start: 0.8145 (t) cc_final: 0.7843 (p) REVERT: AY 1 MET cc_start: 0.5051 (mmt) cc_final: 0.4390 (mmt) REVERT: AY 3 ILE cc_start: 0.8606 (mt) cc_final: 0.8360 (mt) REVERT: A1 1 MET cc_start: 0.6633 (mmt) cc_final: 0.6423 (mmt) REVERT: A1 3 ILE cc_start: 0.8122 (mm) cc_final: 0.7857 (mp) REVERT: A4 1 MET cc_start: 0.6003 (mmt) cc_final: 0.5097 (mmt) REVERT: A4 3 ILE cc_start: 0.8767 (mt) cc_final: 0.8564 (mt) REVERT: A5 1 MET cc_start: 0.5184 (mmt) cc_final: 0.4503 (mmt) REVERT: A6 10 VAL cc_start: 0.8399 (t) cc_final: 0.8089 (p) REVERT: BA 10 VAL cc_start: 0.8087 (t) cc_final: 0.7872 (p) outliers start: 120 outliers final: 112 residues processed: 463 average time/residue: 0.3790 time to fit residues: 276.6216 Evaluate side-chains 487 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 375 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 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 AZ residue 15 ILE 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 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 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 Au residue 14 LEU Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain 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 Ay residue 15 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 A3 residue 15 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 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 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 A0 residue 14 LEU Chi-restraints excluded: chain BA residue 4 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 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 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 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 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: 3.9990 chunk 118 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.118803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.100321 restraints weight = 60236.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.105195 restraints weight = 21945.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.108246 restraints weight = 10689.479| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10112 Z= 0.164 Angle : 0.618 4.457 13376 Z= 0.342 Chirality : 0.060 0.170 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.408 26.678 1344 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 9.01 % Allowed : 29.41 % 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: -3.53 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00370 (10112) covalent geometry : angle 0.61838 (13376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 387 time to evaluate : 1.973 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: 0.6438 (mmt) cc_final: 0.6126 (mmt) REVERT: AU 3 ILE cc_start: 0.8168 (mm) cc_final: 0.7831 (mp) REVERT: AW 1 MET cc_start: 0.5202 (mmt) cc_final: 0.4069 (mmt) REVERT: AW 3 ILE cc_start: 0.8544 (mt) cc_final: 0.8281 (mp) REVERT: AX 1 MET cc_start: 0.5374 (mmt) cc_final: 0.4479 (mmt) REVERT: AY 1 MET cc_start: 0.4985 (mmt) cc_final: 0.4296 (mmt) REVERT: AZ 3 ILE cc_start: 0.8535 (mt) cc_final: 0.8315 (mt) REVERT: Ay 10 VAL cc_start: 0.7980 (t) cc_final: 0.7748 (p) REVERT: A1 3 ILE cc_start: 0.8161 (mm) cc_final: 0.7881 (mp) REVERT: A4 1 MET cc_start: 0.5814 (mmt) cc_final: 0.5051 (mmt) REVERT: A5 1 MET cc_start: 0.5198 (mmt) cc_final: 0.4540 (mmt) REVERT: A6 10 VAL cc_start: 0.8340 (t) cc_final: 0.8047 (p) REVERT: A8 7 ILE cc_start: 0.8916 (mm) cc_final: 0.8689 (mm) REVERT: BA 10 VAL cc_start: 0.7991 (t) cc_final: 0.7782 (p) outliers start: 98 outliers final: 95 residues processed: 455 average time/residue: 0.3815 time to fit residues: 274.0366 Evaluate side-chains 472 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 377 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain 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 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 Aj residue 13 SER 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 3 ILE 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 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 Ay residue 15 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 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 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 BQ residue 14 LEU Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 15 ILE Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.100972 restraints weight = 59742.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.105861 restraints weight = 21700.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.108924 restraints weight = 10537.382| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10112 Z= 0.155 Angle : 0.614 4.294 13376 Z= 0.337 Chirality : 0.060 0.163 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.160 23.056 1344 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 9.10 % Allowed : 30.15 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), 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 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00350 (10112) covalent geometry : angle 0.61371 (13376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 380 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8093 (mm) cc_final: 0.7795 (mp) REVERT: AW 1 MET cc_start: 0.5337 (mmt) cc_final: 0.4183 (mmt) REVERT: AW 3 ILE cc_start: 0.8499 (mt) cc_final: 0.8226 (mp) REVERT: AX 1 MET cc_start: 0.5498 (mmt) cc_final: 0.4579 (mmt) REVERT: AY 1 MET cc_start: 0.5192 (mmt) cc_final: 0.4620 (mmt) REVERT: AZ 3 ILE cc_start: 0.8524 (mt) cc_final: 0.8290 (mt) REVERT: A1 3 ILE cc_start: 0.8186 (mm) cc_final: 0.7913 (mp) REVERT: A4 1 MET cc_start: 0.5810 (mmt) cc_final: 0.5226 (mmt) REVERT: A5 1 MET cc_start: 0.5426 (mmt) cc_final: 0.4774 (mmt) REVERT: A6 10 VAL cc_start: 0.8339 (t) cc_final: 0.8033 (p) REVERT: BA 10 VAL cc_start: 0.8039 (t) cc_final: 0.7814 (p) outliers start: 99 outliers final: 98 residues processed: 448 average time/residue: 0.4078 time to fit residues: 292.4510 Evaluate side-chains 477 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 379 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ai residue 13 SER 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 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 Ay residue 15 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 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 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 BK residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 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 BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BT residue 15 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.126827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.103496 restraints weight = 62289.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.108318 restraints weight = 23546.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.111376 restraints weight = 11939.664| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10112 Z= 0.161 Angle : 0.617 4.388 13376 Z= 0.338 Chirality : 0.060 0.166 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.039 23.444 1344 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 27.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 9.56 % Allowed : 29.69 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.52 (0.18), 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 0.005 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00362 (10112) covalent geometry : angle 0.61668 (13376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 381 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8115 (mm) cc_final: 0.7780 (mp) REVERT: AW 1 MET cc_start: 0.5144 (mmt) cc_final: 0.4231 (mmt) REVERT: AX 1 MET cc_start: 0.5292 (mmt) cc_final: 0.4410 (mmt) REVERT: AY 1 MET cc_start: 0.5058 (mmt) cc_final: 0.4508 (mmt) REVERT: AZ 3 ILE cc_start: 0.8546 (mt) cc_final: 0.8307 (mt) REVERT: A1 3 ILE cc_start: 0.8152 (mm) cc_final: 0.7857 (mp) REVERT: A4 1 MET cc_start: 0.5709 (mmt) cc_final: 0.5220 (mmt) REVERT: A5 1 MET cc_start: 0.5160 (mmt) cc_final: 0.4528 (mmt) REVERT: A6 10 VAL cc_start: 0.8333 (t) cc_final: 0.8056 (p) REVERT: BA 10 VAL cc_start: 0.8002 (t) cc_final: 0.7795 (p) outliers start: 104 outliers final: 100 residues processed: 455 average time/residue: 0.3997 time to fit residues: 289.9301 Evaluate side-chains 479 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 379 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain 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 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 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 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 Ay residue 15 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 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 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 BK residue 13 SER Chi-restraints excluded: chain BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain 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 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 BQ residue 14 LEU Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 8 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 BT residue 15 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Am 17 GLN BJ 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.124062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.101268 restraints weight = 62441.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.106060 restraints weight = 23406.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.109088 restraints weight = 11796.512| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10112 Z= 0.129 Angle : 0.605 3.906 13376 Z= 0.330 Chirality : 0.061 0.162 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.819 19.520 1344 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 8.00 % Allowed : 31.89 % Favored : 60.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -2.64 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00293 (10112) covalent geometry : angle 0.60527 (13376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 3 ILE cc_start: 0.8146 (mm) cc_final: 0.7844 (mp) REVERT: AW 1 MET cc_start: 0.5434 (mmt) cc_final: 0.4497 (mmt) REVERT: AX 1 MET cc_start: 0.5508 (mmt) cc_final: 0.4570 (mmt) REVERT: AY 1 MET cc_start: 0.5247 (mmt) cc_final: 0.4713 (mmt) REVERT: AZ 3 ILE cc_start: 0.8523 (mt) cc_final: 0.8282 (mt) REVERT: A1 3 ILE cc_start: 0.8089 (mm) cc_final: 0.7817 (mp) REVERT: A4 1 MET cc_start: 0.5855 (mmt) cc_final: 0.5409 (mmt) REVERT: A5 1 MET cc_start: 0.5394 (mmt) cc_final: 0.4677 (mmt) REVERT: BA 10 VAL cc_start: 0.8094 (t) cc_final: 0.7874 (p) outliers start: 87 outliers final: 86 residues processed: 445 average time/residue: 0.3849 time to fit residues: 271.3489 Evaluate side-chains 464 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain 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 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 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 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 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 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 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 BL residue 8 ILE Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER 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 8 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 15 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.116589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.098292 restraints weight = 61861.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.102924 restraints weight = 22163.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.105823 restraints weight = 10834.108| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10112 Z= 0.133 Angle : 0.608 4.745 13376 Z= 0.331 Chirality : 0.061 0.162 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.696 19.191 1344 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 27.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 8.00 % Allowed : 32.17 % Favored : 59.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 Details of bonding type rmsd covalent geometry : bond 0.00301 (10112) covalent geometry : angle 0.60833 (13376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8849.53 seconds wall clock time: 154 minutes 25.92 seconds (9265.92 seconds total)