Starting phenix.real_space_refine on Wed Sep 17 08:19:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.map" model { file = "/net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auf_43878/09_2025/9auf_43878.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 192 5.49 5 S 12 5.16 5 C 3838 2.51 5 N 1329 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7251 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3193 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 3 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3121 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 76, 'rna3p_pyr': 58} Link IDs: {'rna2p': 12, 'rna3p': 133} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "c" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.03, per 1000 atoms: 0.28 Number of scatterers: 7251 At special positions: 0 Unit cell: (82.4868, 101.65, 125.813, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 192 15.00 O 1880 8.00 N 1329 7.00 C 3838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 268.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 44.2% alpha, 12.9% beta 81 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 75 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.556A pdb=" N ILE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.570A pdb=" N VAL A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.676A pdb=" N GLU A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.271A pdb=" N VAL A 657 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A 695 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 659 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 733 through 734 removed outlier: 6.212A pdb=" N GLU A 723 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 713 " --> pdb=" O GLU A 723 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1174 1.33 - 1.45: 2875 1.45 - 1.57: 3328 1.57 - 1.69: 380 1.69 - 1.81: 18 Bond restraints: 7775 Sorted by residual: bond pdb=" N ALA A 724 " pdb=" CA ALA A 724 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.79e+00 bond pdb=" C GLU A 723 " pdb=" N ALA A 724 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.32e-02 5.74e+03 2.91e+00 bond pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 1.607 1.631 -0.024 1.50e-02 4.44e+03 2.51e+00 bond pdb=" C3' G B 142 " pdb=" O3' G B 142 " ideal model delta sigma weight residual 1.427 1.450 -0.023 1.50e-02 4.44e+03 2.32e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 11205 2.45 - 4.90: 146 4.90 - 7.35: 8 7.35 - 9.80: 2 9.80 - 12.25: 3 Bond angle restraints: 11364 Sorted by residual: angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 126.25 -12.25 1.50e+00 4.44e-01 6.67e+01 angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 118.94 -10.74 1.50e+00 4.44e-01 5.12e+01 angle pdb=" C3' U B 92 " pdb=" O3' U B 92 " pdb=" P U B 93 " ideal model delta sigma weight residual 120.20 127.18 -6.98 1.50e+00 4.44e-01 2.17e+01 angle pdb=" C3' G B 142 " pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 120.20 126.60 -6.40 1.50e+00 4.44e-01 1.82e+01 angle pdb=" O3' G B 122 " pdb=" C3' G B 122 " pdb=" C2' G B 122 " ideal model delta sigma weight residual 113.70 120.06 -6.36 1.50e+00 4.44e-01 1.80e+01 ... (remaining 11359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 4289 34.45 - 68.89: 444 68.89 - 103.34: 40 103.34 - 137.78: 1 137.78 - 172.23: 3 Dihedral angle restraints: 4777 sinusoidal: 3642 harmonic: 1135 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 44.23 -172.23 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual -106.00 -178.82 72.82 1 1.70e+01 3.46e-03 2.34e+01 dihedral pdb=" CA GLU A 723 " pdb=" C GLU A 723 " pdb=" N ALA A 724 " pdb=" CA ALA A 724 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1377 0.219 - 0.437: 4 0.437 - 0.656: 0 0.656 - 0.875: 0 0.875 - 1.093: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.34 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" P DT c 23 " pdb=" OP1 DT c 23 " pdb=" OP2 DT c 23 " pdb=" O5' DT c 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.68 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1379 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " -0.072 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" N9 G B 142 " 0.084 2.00e-02 2.50e+03 pdb=" C8 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 142 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 142 " -0.022 2.00e-02 2.50e+03 pdb=" N1 G B 142 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G B 142 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 142 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 142 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 142 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 723 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C GLU A 723 " 0.090 2.00e-02 2.50e+03 pdb=" O GLU A 723 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA A 724 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 111 " -0.027 2.00e-02 2.50e+03 1.20e-02 3.96e+00 pdb=" N9 A B 111 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A B 111 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 111 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 111 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 111 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 111 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A B 111 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 111 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A B 111 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 111 " 0.003 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2084 2.84 - 3.36: 5888 3.36 - 3.87: 15215 3.87 - 4.39: 17526 4.39 - 4.90: 22950 Nonbonded interactions: 63663 Sorted by model distance: nonbonded pdb=" N2 G B 38 " pdb=" OP2 A B 41 " model vdw 2.331 3.120 nonbonded pdb=" O VAL A 583 " pdb=" NH1 ARG A 589 " model vdw 2.334 3.120 nonbonded pdb=" N2 G B 117 " pdb=" OP2 A B 120 " model vdw 2.363 3.120 nonbonded pdb=" NE ARG A 170 " pdb=" OP1 G B 16 " model vdw 2.365 3.120 nonbonded pdb=" OE1 GLU A 586 " pdb=" NH2 ARG A 589 " model vdw 2.386 3.120 ... (remaining 63658 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.005 0.066 7775 Z= 0.221 Angle : 0.731 12.254 11364 Z= 0.403 Chirality : 0.052 1.093 1382 Planarity : 0.007 0.075 747 Dihedral : 21.696 172.226 4039 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.57 % Allowed : 11.65 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.40), residues: 381 helix: 0.10 (0.39), residues: 146 sheet: -0.06 (0.72), residues: 46 loop : -0.17 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 163 TYR 0.020 0.003 TYR A 250 PHE 0.024 0.003 PHE A 596 HIS 0.006 0.002 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 7775) covalent geometry : angle 0.73062 (11364) hydrogen bonds : bond 0.11875 ( 336) hydrogen bonds : angle 4.37466 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (tp40) REVERT: A 148 MET cc_start: 0.8397 (mtp) cc_final: 0.7920 (mtp) REVERT: A 159 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7659 (mtmt) REVERT: A 586 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7572 (tt0) REVERT: A 697 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7404 (mptt) REVERT: A 712 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6652 (ttt180) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.8990 time to fit residues: 50.3698 Evaluate side-chains 48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.189311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136033 restraints weight = 6207.746| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.05 r_work: 0.3322 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7775 Z= 0.242 Angle : 0.623 11.559 11364 Z= 0.344 Chirality : 0.045 0.904 1382 Planarity : 0.006 0.051 747 Dihedral : 22.431 168.798 3169 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.69 % Allowed : 11.93 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.43), residues: 381 helix: 1.13 (0.41), residues: 148 sheet: -0.32 (0.75), residues: 44 loop : -0.14 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 51 TYR 0.014 0.002 TYR A 169 PHE 0.013 0.002 PHE A 648 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 7775) covalent geometry : angle 0.62301 (11364) hydrogen bonds : bond 0.04957 ( 336) hydrogen bonds : angle 3.34340 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8500 (ttp-170) REVERT: A 50 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: A 159 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7702 (mtmt) REVERT: A 586 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7625 (tt0) REVERT: A 625 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 697 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7425 (mptt) REVERT: A 712 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6882 (ttm-80) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.8212 time to fit residues: 48.5944 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.189467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137353 restraints weight = 6131.169| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.01 r_work: 0.3351 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7775 Z= 0.196 Angle : 0.577 11.180 11364 Z= 0.322 Chirality : 0.042 0.851 1382 Planarity : 0.005 0.037 747 Dihedral : 22.365 167.192 3169 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.55 % Allowed : 11.65 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.43), residues: 381 helix: 1.68 (0.41), residues: 148 sheet: -0.47 (0.76), residues: 44 loop : -0.02 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 163 TYR 0.012 0.001 TYR A 169 PHE 0.012 0.002 PHE A 648 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7775) covalent geometry : angle 0.57702 (11364) hydrogen bonds : bond 0.04436 ( 336) hydrogen bonds : angle 3.15178 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.237 Fit side-chains REVERT: A 48 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8475 (ttp-170) REVERT: A 159 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7635 (mtmt) REVERT: A 211 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6965 (pp) REVERT: A 586 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7609 (tt0) REVERT: A 611 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 625 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 697 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7424 (mptt) REVERT: A 712 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6921 (ttm-80) REVERT: A 714 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7649 (tptt) outliers start: 16 outliers final: 5 residues processed: 57 average time/residue: 0.8889 time to fit residues: 52.6284 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.192349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139766 restraints weight = 6213.720| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 0.93 r_work: 0.3373 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.164 Angle : 0.538 10.485 11364 Z= 0.302 Chirality : 0.039 0.752 1382 Planarity : 0.004 0.032 747 Dihedral : 22.249 166.354 3166 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.26 % Allowed : 12.78 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.43), residues: 381 helix: 2.09 (0.41), residues: 149 sheet: -0.47 (0.79), residues: 42 loop : 0.10 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 163 TYR 0.010 0.001 TYR A 169 PHE 0.010 0.001 PHE A 648 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7775) covalent geometry : angle 0.53790 (11364) hydrogen bonds : bond 0.03995 ( 336) hydrogen bonds : angle 3.00259 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.189 Fit side-chains REVERT: A 48 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8470 (ttp-170) REVERT: A 88 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8298 (t) REVERT: A 159 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7639 (mtmt) REVERT: A 211 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7070 (pp) REVERT: A 581 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8018 (t0) REVERT: A 586 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7632 (tt0) REVERT: A 607 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 611 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 625 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7975 (m) REVERT: A 687 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6440 (pt0) REVERT: A 697 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7558 (mptt) REVERT: A 714 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7675 (tptt) REVERT: A 742 LYS cc_start: 0.7937 (tttp) cc_final: 0.7489 (tptt) outliers start: 15 outliers final: 2 residues processed: 59 average time/residue: 0.8737 time to fit residues: 53.4998 Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.190245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137447 restraints weight = 6144.797| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 0.93 r_work: 0.3347 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7775 Z= 0.210 Angle : 0.570 10.976 11364 Z= 0.317 Chirality : 0.042 0.819 1382 Planarity : 0.004 0.035 747 Dihedral : 22.296 167.210 3166 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.55 % Allowed : 13.07 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.44), residues: 381 helix: 2.08 (0.42), residues: 149 sheet: -0.40 (0.80), residues: 42 loop : 0.11 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.014 0.001 TYR A 70 PHE 0.011 0.001 PHE A 648 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 7775) covalent geometry : angle 0.57009 (11364) hydrogen bonds : bond 0.04324 ( 336) hydrogen bonds : angle 3.05122 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.184 Fit side-chains REVERT: A 48 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8464 (ttp-170) REVERT: A 142 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: A 159 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7667 (mtmt) REVERT: A 211 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7100 (pp) REVERT: A 586 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7686 (tt0) REVERT: A 611 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 625 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7981 (m) REVERT: A 697 LYS cc_start: 0.7924 (mmtp) cc_final: 0.7545 (mptt) REVERT: A 714 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7688 (tptt) REVERT: A 716 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7720 (pp) REVERT: A 742 LYS cc_start: 0.7956 (tttp) cc_final: 0.7515 (tptt) outliers start: 16 outliers final: 4 residues processed: 59 average time/residue: 0.9268 time to fit residues: 56.6798 Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 687 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.191376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138993 restraints weight = 6122.008| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.97 r_work: 0.3360 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.166 Angle : 0.547 10.752 11364 Z= 0.307 Chirality : 0.040 0.789 1382 Planarity : 0.004 0.032 747 Dihedral : 22.283 166.867 3166 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.69 % Allowed : 13.64 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.44), residues: 381 helix: 2.21 (0.42), residues: 149 sheet: -0.45 (0.80), residues: 42 loop : 0.12 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.012 0.001 TYR A 70 PHE 0.014 0.001 PHE A 235 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7775) covalent geometry : angle 0.54723 (11364) hydrogen bonds : bond 0.04130 ( 336) hydrogen bonds : angle 3.01772 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.212 Fit side-chains REVERT: A 48 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8456 (ttp-170) REVERT: A 142 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8193 (mtpt) REVERT: A 159 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7658 (mtmt) REVERT: A 211 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7047 (pp) REVERT: A 586 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7657 (tt0) REVERT: A 607 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (mt) REVERT: A 611 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 621 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6924 (mtmt) REVERT: A 625 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 697 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7458 (mptt) REVERT: A 716 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 742 LYS cc_start: 0.7925 (tttp) cc_final: 0.7482 (tptt) outliers start: 13 outliers final: 3 residues processed: 52 average time/residue: 0.9489 time to fit residues: 51.1830 Evaluate side-chains 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.192590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140289 restraints weight = 6174.998| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 0.99 r_work: 0.3361 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.137 Angle : 0.532 10.530 11364 Z= 0.300 Chirality : 0.038 0.758 1382 Planarity : 0.004 0.030 747 Dihedral : 22.271 166.559 3166 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.69 % Allowed : 13.64 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.44), residues: 381 helix: 2.29 (0.42), residues: 149 sheet: -0.49 (0.79), residues: 42 loop : 0.15 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.010 0.001 TYR A 70 PHE 0.010 0.001 PHE A 235 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7775) covalent geometry : angle 0.53189 (11364) hydrogen bonds : bond 0.03954 ( 336) hydrogen bonds : angle 2.98000 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.136 Fit side-chains REVERT: A 48 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (ttp-170) REVERT: A 88 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8295 (t) REVERT: A 142 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8231 (mtpt) REVERT: A 159 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7672 (mtmt) REVERT: A 211 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 586 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7662 (tt0) REVERT: A 607 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7184 (mt) REVERT: A 611 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 625 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 697 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7550 (mptt) REVERT: A 742 LYS cc_start: 0.7939 (tttp) cc_final: 0.7497 (tptt) outliers start: 13 outliers final: 4 residues processed: 53 average time/residue: 0.8645 time to fit residues: 47.4763 Evaluate side-chains 53 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.185201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131536 restraints weight = 6220.358| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.13 r_work: 0.3276 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7775 Z= 0.217 Angle : 0.570 10.999 11364 Z= 0.317 Chirality : 0.042 0.828 1382 Planarity : 0.004 0.034 747 Dihedral : 22.288 167.045 3166 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.41 % Allowed : 14.49 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.44), residues: 381 helix: 2.18 (0.42), residues: 149 sheet: -0.46 (0.80), residues: 42 loop : 0.05 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.014 0.001 TYR A 70 PHE 0.010 0.001 PHE A 648 HIS 0.005 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7775) covalent geometry : angle 0.57031 (11364) hydrogen bonds : bond 0.04295 ( 336) hydrogen bonds : angle 3.03668 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.150 Fit side-chains REVERT: A 48 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (ttp-170) REVERT: A 142 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: A 159 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7604 (mtmt) REVERT: A 211 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7012 (pp) REVERT: A 586 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7624 (tt0) REVERT: A 611 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 621 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6938 (mtmt) REVERT: A 625 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7941 (m) REVERT: A 697 LYS cc_start: 0.7881 (mmtp) cc_final: 0.7485 (mptt) REVERT: A 716 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7717 (pp) REVERT: A 742 LYS cc_start: 0.7910 (tttp) cc_final: 0.7464 (tptt) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.8932 time to fit residues: 48.9561 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.188365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133901 restraints weight = 6124.208| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.91 r_work: 0.3321 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7775 Z= 0.147 Angle : 0.535 10.586 11364 Z= 0.302 Chirality : 0.039 0.767 1382 Planarity : 0.004 0.040 747 Dihedral : 22.273 166.306 3166 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.44), residues: 381 helix: 2.20 (0.42), residues: 149 sheet: -0.44 (0.80), residues: 42 loop : 0.13 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 163 TYR 0.010 0.001 TYR A 70 PHE 0.010 0.001 PHE A 648 HIS 0.003 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7775) covalent geometry : angle 0.53510 (11364) hydrogen bonds : bond 0.04009 ( 336) hydrogen bonds : angle 3.07236 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.201 Fit side-chains REVERT: A 48 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8460 (ttp-170) REVERT: A 142 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8150 (mtpt) REVERT: A 159 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7636 (mtmt) REVERT: A 211 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.6987 (pp) REVERT: A 586 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7641 (tt0) REVERT: A 611 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 621 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6994 (mtmt) REVERT: A 625 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7945 (m) REVERT: A 697 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7522 (mptt) REVERT: A 716 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7590 (pp) REVERT: A 742 LYS cc_start: 0.7918 (tttp) cc_final: 0.7485 (tptt) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.8960 time to fit residues: 48.3577 Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.185165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131678 restraints weight = 6153.620| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.07 r_work: 0.3275 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7775 Z= 0.208 Angle : 0.571 11.069 11364 Z= 0.318 Chirality : 0.042 0.836 1382 Planarity : 0.005 0.043 747 Dihedral : 22.307 166.891 3166 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.12 % Allowed : 15.06 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.44), residues: 381 helix: 2.04 (0.42), residues: 149 sheet: -0.48 (0.80), residues: 42 loop : 0.07 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 163 TYR 0.014 0.002 TYR A 70 PHE 0.009 0.001 PHE A 648 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7775) covalent geometry : angle 0.57147 (11364) hydrogen bonds : bond 0.04307 ( 336) hydrogen bonds : angle 3.10769 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.126 Fit side-chains REVERT: A 48 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8473 (ttp-170) REVERT: A 142 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: A 159 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7655 (mtmt) REVERT: A 211 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 586 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7676 (tt0) REVERT: A 611 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 621 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7020 (mtmt) REVERT: A 625 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7965 (m) REVERT: A 697 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7526 (mptt) REVERT: A 716 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7710 (pp) REVERT: A 742 LYS cc_start: 0.7933 (tttp) cc_final: 0.7503 (tptt) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.7725 time to fit residues: 45.6469 Evaluate side-chains 55 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 741 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.0470 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.186427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131894 restraints weight = 6131.150| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.01 r_work: 0.3287 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 7775 Z= 0.232 Angle : 0.931 59.143 11364 Z= 0.553 Chirality : 0.043 0.830 1382 Planarity : 0.005 0.041 747 Dihedral : 22.309 166.902 3166 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.12 % Allowed : 15.34 % Favored : 81.53 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.44), residues: 381 helix: 2.03 (0.42), residues: 149 sheet: -0.48 (0.80), residues: 42 loop : 0.07 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 163 TYR 0.014 0.001 TYR A 70 PHE 0.009 0.001 PHE A 648 HIS 0.004 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 7775) covalent geometry : angle 0.93082 (11364) hydrogen bonds : bond 0.04264 ( 336) hydrogen bonds : angle 3.11805 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.58 seconds wall clock time: 50 minutes 52.46 seconds (3052.46 seconds total)