Starting phenix.real_space_refine on Sun Sep 29 03:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_43835.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_43835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_43835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_43835.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atw_43835/09_2024/9atw_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-5461/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: 4.82, 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: 5.60 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: 2.52 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: 6.71 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A0' selection = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'A4' selection = chain 'A5' selection = chain 'A6' selection = chain 'A7' selection = chain 'A8' selection = chain 'A9' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' selection = chain 'BJ' selection = chain 'BK' selection = chain 'BL' selection = chain 'BM' selection = chain 'BN' selection = chain 'BO' selection = chain 'BP' selection = chain 'BQ' selection = chain 'BR' selection = chain 'BS' selection = chain 'BT' selection = chain 'BU' selection = chain 'BV' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 33.250 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.140 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.032 10112 Z= 0.676 Angle : 2.181 6.598 13376 Z= 1.413 Chirality : 0.135 0.274 1728 Planarity : 0.009 0.022 1536 Dihedral : 15.033 50.808 3904 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.12), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.10), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.009 PHEA4 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 1.808 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: 0.3219 time to fit residues: 306.9989 Evaluate side-chains 482 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10112 Z= 0.158 Angle : 0.717 5.683 13376 Z= 0.405 Chirality : 0.066 0.164 1728 Planarity : 0.002 0.014 1536 Dihedral : 10.483 21.438 1344 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.71 % Allowed : 19.21 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.12), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.09), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHEBP 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 440 time to evaluate : 2.045 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: 0.6335 (mmt) cc_final: 0.5781 (mmt) REVERT: AX 1 MET cc_start: 0.6192 (mmt) cc_final: 0.5780 (mmt) REVERT: AY 1 MET cc_start: 0.5970 (mmt) cc_final: 0.5409 (mmt) REVERT: A1 1 MET cc_start: 0.7085 (mmt) cc_final: 0.6538 (mmt) REVERT: A4 1 MET cc_start: 0.6358 (mmt) cc_final: 0.5904 (mmt) REVERT: A5 1 MET cc_start: 0.6024 (mmt) cc_final: 0.5383 (mmt) REVERT: A6 1 MET cc_start: 0.5978 (mmt) cc_final: 0.5436 (mmt) REVERT: A7 8 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7757 (mt) REVERT: BF 13 SER cc_start: 0.8923 (p) cc_final: 0.8708 (m) outliers start: 73 outliers final: 56 residues processed: 461 average time/residue: 0.3347 time to fit residues: 248.8082 Evaluate side-chains 458 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 401 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 A7 residue 8 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 64 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 93 optimal weight: 3.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10112 Z= 0.211 Angle : 0.699 5.138 13376 Z= 0.389 Chirality : 0.064 0.170 1728 Planarity : 0.002 0.012 1536 Dihedral : 8.913 18.853 1344 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 8.18 % Allowed : 21.78 % Favored : 70.04 % 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: -3.38 (0.14), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.11), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHEAw 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 428 time to evaluate : 1.622 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: AU 1 MET cc_start: 0.6899 (mmt) cc_final: 0.6486 (mmt) REVERT: AW 1 MET cc_start: 0.6610 (mmt) cc_final: 0.5744 (mmt) REVERT: AX 1 MET cc_start: 0.6390 (mmt) cc_final: 0.5858 (mmt) REVERT: AY 1 MET cc_start: 0.5945 (mmt) cc_final: 0.5411 (mmt) REVERT: Aa 1 MET cc_start: 0.6020 (mmt) cc_final: 0.5503 (mmt) REVERT: Ad 10 VAL cc_start: 0.8392 (t) cc_final: 0.8159 (p) REVERT: A1 1 MET cc_start: 0.7046 (mmt) cc_final: 0.6584 (mmt) REVERT: A4 1 MET cc_start: 0.6489 (mmt) cc_final: 0.5935 (mmt) REVERT: A5 1 MET cc_start: 0.6033 (mmt) cc_final: 0.5529 (mmt) REVERT: A6 1 MET cc_start: 0.6061 (mmt) cc_final: 0.5450 (mmt) REVERT: A6 10 VAL cc_start: 0.8512 (t) cc_final: 0.8251 (p) outliers start: 89 outliers final: 86 residues processed: 461 average time/residue: 0.3500 time to fit residues: 258.2284 Evaluate side-chains 494 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 408 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 8 ILE Chi-restraints excluded: chain Aa residue 14 LEU Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 8 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 13 SER Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain 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 At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 13 SER Chi-restraints excluded: chain 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 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 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 8 ILE Chi-restraints excluded: chain A7 residue 14 LEU 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 BS residue 14 LEU Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 13 SER Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10112 Z= 0.236 Angle : 0.673 4.843 13376 Z= 0.375 Chirality : 0.061 0.160 1728 Planarity : 0.002 0.011 1536 Dihedral : 8.457 27.715 1344 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 9.38 % Allowed : 26.65 % Favored : 63.97 % 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: -3.46 (0.16), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.12), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHEAY 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 408 time to evaluate : 1.733 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: AU 1 MET cc_start: 0.7002 (mmt) cc_final: 0.6787 (mmt) REVERT: AW 1 MET cc_start: 0.6560 (mmt) cc_final: 0.5991 (mmt) REVERT: AX 1 MET cc_start: 0.6472 (mmt) cc_final: 0.5821 (mmt) REVERT: AY 1 MET cc_start: 0.6199 (mmt) cc_final: 0.5603 (mmt) REVERT: Ad 10 VAL cc_start: 0.8479 (t) cc_final: 0.8168 (p) REVERT: A1 1 MET cc_start: 0.7106 (mmt) cc_final: 0.6654 (mmt) REVERT: A4 1 MET cc_start: 0.6748 (mmt) cc_final: 0.5959 (mmt) REVERT: A5 1 MET cc_start: 0.6140 (mmt) cc_final: 0.5644 (mmt) REVERT: A6 10 VAL cc_start: 0.8529 (t) cc_final: 0.8294 (p) outliers start: 102 outliers final: 95 residues processed: 461 average time/residue: 0.3551 time to fit residues: 261.4324 Evaluate side-chains 485 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 390 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 AY residue 4 ILE Chi-restraints excluded: chain AY residue 8 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AY residue 14 LEU Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 8 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain 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 Aj residue 13 SER 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 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 Au residue 13 SER Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Aw residue 13 SER Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A8 residue 13 SER Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 14 LEU Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BC residue 13 SER Chi-restraints excluded: chain BD residue 13 SER Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BQ residue 14 LEU Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 13 SER Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10112 Z= 0.141 Angle : 0.609 4.792 13376 Z= 0.339 Chirality : 0.061 0.166 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.583 20.130 1344 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 9.47 % Allowed : 26.01 % 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 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAY 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 407 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AU 1 MET cc_start: 0.6973 (mmt) cc_final: 0.6740 (mmt) REVERT: AW 1 MET cc_start: 0.6574 (mmt) cc_final: 0.5844 (mmt) REVERT: AX 1 MET cc_start: 0.6581 (mmt) cc_final: 0.5948 (mmt) REVERT: AY 1 MET cc_start: 0.6095 (mmt) cc_final: 0.5441 (mmt) REVERT: A1 1 MET cc_start: 0.7126 (mmt) cc_final: 0.6762 (mmt) REVERT: A4 1 MET cc_start: 0.6881 (mmt) cc_final: 0.5936 (mmt) REVERT: A5 1 MET cc_start: 0.6148 (mmt) cc_final: 0.5574 (mmt) REVERT: A6 10 VAL cc_start: 0.8463 (t) cc_final: 0.8220 (p) outliers start: 103 outliers final: 93 residues processed: 468 average time/residue: 0.3596 time to fit residues: 272.1829 Evaluate side-chains 480 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 387 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 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 Aj residue 13 SER 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 13 SER Chi-restraints excluded: chain At residue 14 LEU Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 13 SER Chi-restraints excluded: chain 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 Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 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 A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BD residue 15 ILE Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BL residue 14 LEU Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain 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 41 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10112 Z= 0.234 Angle : 0.659 4.556 13376 Z= 0.365 Chirality : 0.060 0.165 1728 Planarity : 0.002 0.009 1536 Dihedral : 7.877 30.301 1344 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 11.12 % Allowed : 25.83 % Favored : 63.05 % 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 *********************** 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 fitting. rotamer outliers: 121 poor density : 388 time to evaluate : 1.833 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: AW 1 MET cc_start: 0.6764 (mmt) cc_final: 0.5714 (mmt) REVERT: AX 1 MET cc_start: 0.6784 (mmt) cc_final: 0.6103 (mmt) REVERT: AX 10 VAL cc_start: 0.8675 (t) cc_final: 0.8414 (p) REVERT: AY 1 MET cc_start: 0.6286 (mmt) cc_final: 0.5648 (mmt) REVERT: A4 1 MET cc_start: 0.7082 (mmt) cc_final: 0.6170 (mmt) REVERT: A5 1 MET cc_start: 0.6333 (mmt) cc_final: 0.5712 (mmt) REVERT: A6 10 VAL cc_start: 0.8539 (t) cc_final: 0.8294 (p) outliers start: 121 outliers final: 117 residues processed: 466 average time/residue: 0.3779 time to fit residues: 280.5612 Evaluate side-chains 496 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 379 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 8 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 8 ILE Chi-restraints excluded: chain AX residue 14 LEU 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 14 LEU Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ab residue 14 LEU Chi-restraints excluded: chain Ac residue 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Aj residue 13 SER Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain Am residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 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 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A8 residue 13 SER Chi-restraints excluded: chain A8 residue 14 LEU Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A9 residue 14 LEU Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BB residue 8 ILE Chi-restraints excluded: chain BD residue 15 ILE Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BK residue 13 SER Chi-restraints excluded: chain BK residue 14 LEU Chi-restraints excluded: chain BL residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 14 LEU Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BP residue 14 LEU Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 15 ILE Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6856 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= 0.172 Angle : 0.620 4.348 13376 Z= 0.342 Chirality : 0.060 0.160 1728 Planarity : 0.002 0.010 1536 Dihedral : 7.403 24.962 1344 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 9.74 % Allowed : 28.22 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.17), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 391 time to evaluate : 1.860 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: AW 1 MET cc_start: 0.6721 (mmt) cc_final: 0.5698 (mmt) REVERT: AX 1 MET cc_start: 0.6736 (mmt) cc_final: 0.6007 (mmt) REVERT: AX 10 VAL cc_start: 0.8496 (t) cc_final: 0.8248 (p) REVERT: AY 1 MET cc_start: 0.6320 (mmt) cc_final: 0.5705 (mmt) REVERT: A4 1 MET cc_start: 0.7009 (mmt) cc_final: 0.6220 (mmt) REVERT: A5 1 MET cc_start: 0.6476 (mmt) cc_final: 0.5849 (mmt) REVERT: A6 10 VAL cc_start: 0.8540 (t) cc_final: 0.8294 (p) outliers start: 106 outliers final: 102 residues processed: 462 average time/residue: 0.3740 time to fit residues: 273.2294 Evaluate side-chains 486 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 384 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ad residue 14 LEU Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 14 LEU Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Ak residue 13 SER Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 8 ILE Chi-restraints excluded: chain As residue 14 LEU Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Av residue 14 LEU Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Aw residue 13 SER Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain Ax residue 14 LEU Chi-restraints excluded: chain Ay residue 4 ILE Chi-restraints excluded: chain Ay residue 13 SER Chi-restraints excluded: chain Ay residue 14 LEU Chi-restraints excluded: chain Az residue 12 LYS Chi-restraints excluded: chain Az residue 14 LEU Chi-restraints excluded: chain A1 residue 13 SER Chi-restraints excluded: chain A2 residue 4 ILE Chi-restraints excluded: chain A2 residue 13 SER Chi-restraints excluded: chain A3 residue 4 ILE Chi-restraints excluded: chain A3 residue 8 ILE Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 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 BL 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 8 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BN residue 14 LEU Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 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 BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 112 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Am 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10112 Z= 0.114 Angle : 0.595 4.148 13376 Z= 0.326 Chirality : 0.061 0.163 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.937 18.484 1344 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 7.81 % Allowed : 30.42 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHEAy 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 389 time to evaluate : 1.810 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: AW 1 MET cc_start: 0.6612 (mmt) cc_final: 0.5590 (mmt) REVERT: AX 1 MET cc_start: 0.6780 (mmt) cc_final: 0.6033 (mmt) REVERT: AY 1 MET cc_start: 0.6342 (mmt) cc_final: 0.5744 (mmt) REVERT: A4 1 MET cc_start: 0.6875 (mmt) cc_final: 0.6224 (mmt) REVERT: A5 1 MET cc_start: 0.6546 (mmt) cc_final: 0.5890 (mmt) REVERT: A5 15 ILE cc_start: 0.8122 (tt) cc_final: 0.7846 (tt) REVERT: A6 10 VAL cc_start: 0.8476 (t) cc_final: 0.8214 (p) outliers start: 85 outliers final: 82 residues processed: 455 average time/residue: 0.3779 time to fit residues: 272.6620 Evaluate side-chains 465 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 383 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 13 SER Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain AZ residue 13 SER Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 15 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 8 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain 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 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 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 A7 residue 8 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BB residue 8 ILE Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 13 SER Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10112 Z= 0.159 Angle : 0.610 4.351 13376 Z= 0.334 Chirality : 0.060 0.160 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.947 21.328 1344 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 8.64 % Allowed : 30.24 % Favored : 61.12 % 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: -3.48 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.13), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHEAV 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 389 time to evaluate : 1.821 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: AW 1 MET cc_start: 0.6697 (mmt) cc_final: 0.5640 (mmt) REVERT: AX 1 MET cc_start: 0.6701 (mmt) cc_final: 0.5972 (mmt) REVERT: AY 1 MET cc_start: 0.6470 (mmt) cc_final: 0.5950 (mmt) REVERT: A4 1 MET cc_start: 0.6964 (mmt) cc_final: 0.6383 (mmt) REVERT: A5 1 MET cc_start: 0.6471 (mmt) cc_final: 0.5802 (mmt) REVERT: A5 15 ILE cc_start: 0.8135 (tt) cc_final: 0.7875 (tt) REVERT: A6 10 VAL cc_start: 0.8508 (t) cc_final: 0.8253 (p) outliers start: 94 outliers final: 92 residues processed: 456 average time/residue: 0.3778 time to fit residues: 271.5567 Evaluate side-chains 477 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 385 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 3 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 14 LEU Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain Al residue 13 SER Chi-restraints excluded: chain An residue 13 SER Chi-restraints excluded: chain Ap residue 8 ILE Chi-restraints excluded: chain Ap residue 14 LEU Chi-restraints excluded: chain Aq residue 13 SER Chi-restraints excluded: chain Aq residue 14 LEU Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 8 ILE Chi-restraints excluded: chain 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 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 13 SER Chi-restraints excluded: chain A4 residue 4 ILE Chi-restraints excluded: chain A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A5 residue 14 LEU Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 ILE Chi-restraints excluded: chain A8 residue 4 ILE Chi-restraints excluded: chain A9 residue 4 ILE Chi-restraints excluded: chain A0 residue 4 ILE Chi-restraints excluded: chain BA residue 4 ILE Chi-restraints excluded: chain BB residue 8 ILE Chi-restraints excluded: chain BD residue 3 ILE Chi-restraints excluded: chain BF residue 15 ILE Chi-restraints excluded: chain BG residue 8 ILE Chi-restraints excluded: chain BJ residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BP residue 14 LEU Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BT residue 14 LEU Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 15 ILE Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10112 Z= 0.126 Angle : 0.601 4.749 13376 Z= 0.327 Chirality : 0.061 0.167 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.767 18.685 1344 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.81 % Allowed : 31.34 % Favored : 60.85 % 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: -3.46 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 388 time to evaluate : 1.824 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: AW 1 MET cc_start: 0.6640 (mmt) cc_final: 0.5563 (mmt) REVERT: AX 1 MET cc_start: 0.6657 (mmt) cc_final: 0.5936 (mmt) REVERT: AY 1 MET cc_start: 0.6439 (mmt) cc_final: 0.5884 (mmt) REVERT: Aw 8 ILE cc_start: 0.8685 (mp) cc_final: 0.8406 (pt) REVERT: A4 1 MET cc_start: 0.6946 (mmt) cc_final: 0.6411 (mmt) REVERT: A5 1 MET cc_start: 0.6443 (mmt) cc_final: 0.5767 (mmt) REVERT: A5 15 ILE cc_start: 0.8144 (tt) cc_final: 0.7869 (tt) REVERT: A6 10 VAL cc_start: 0.8519 (t) cc_final: 0.8061 (p) outliers start: 85 outliers final: 83 residues processed: 454 average time/residue: 0.3749 time to fit residues: 268.7195 Evaluate side-chains 469 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 386 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AU residue 12 LYS Chi-restraints excluded: chain AU residue 13 SER Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AV residue 13 SER Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AX residue 13 SER Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain AY residue 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 Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 4 ILE Chi-restraints excluded: chain Ag residue 4 ILE Chi-restraints excluded: chain 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 Ar residue 4 ILE Chi-restraints excluded: chain Ar residue 13 SER Chi-restraints excluded: chain Ar residue 14 LEU Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain As residue 8 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain At residue 13 SER Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain Ax residue 4 ILE Chi-restraints excluded: chain Ax residue 13 SER Chi-restraints excluded: chain 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 A4 residue 8 ILE Chi-restraints excluded: chain A4 residue 13 SER Chi-restraints excluded: chain A5 residue 4 ILE Chi-restraints excluded: chain A5 residue 8 ILE Chi-restraints excluded: chain A5 residue 13 SER Chi-restraints excluded: chain A6 residue 4 ILE Chi-restraints excluded: chain A6 residue 13 SER Chi-restraints excluded: chain A7 residue 4 ILE Chi-restraints excluded: chain A7 residue 8 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 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 BL residue 13 SER Chi-restraints excluded: chain BM residue 15 ILE Chi-restraints excluded: chain BN residue 8 ILE Chi-restraints excluded: chain BN residue 13 SER Chi-restraints excluded: chain BO residue 4 ILE Chi-restraints excluded: chain BO residue 13 SER Chi-restraints excluded: chain BO residue 15 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 SER Chi-restraints excluded: chain BQ residue 4 ILE Chi-restraints excluded: chain BR residue 4 ILE Chi-restraints excluded: chain BR residue 13 SER Chi-restraints excluded: chain BR residue 14 LEU Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BT residue 4 ILE Chi-restraints excluded: chain BU residue 4 ILE Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BV residue 12 LYS Chi-restraints excluded: chain BV residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.125375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.102471 restraints weight = 60423.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.107557 restraints weight = 22158.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.110765 restraints weight = 10896.653| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10112 Z= 0.117 Angle : 0.600 4.843 13376 Z= 0.325 Chirality : 0.061 0.163 1728 Planarity : 0.002 0.010 1536 Dihedral : 6.591 18.424 1344 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 7.63 % Allowed : 31.99 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.18), residues: 1216 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEAy 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6373.10 seconds wall clock time: 112 minutes 2.81 seconds (6722.81 seconds total)