Starting phenix.real_space_refine on Tue Feb 11 00:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9g_34566/02_2025/8h9g_34566.cif" } resolution = 2.95 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= 0.000 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 5.03, per 1000 atoms: 1.49 Number of scatterers: 3381 At special positions: 0 Unit cell: (79.57, 101.47, 205.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 634 8.00 N 560 7.00 C 2176 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: 0.80 Conformation dependent library (CDL) restraints added in 385.4 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.970A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 removed outlier: 4.074A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.409A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.761A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.810A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.735A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.538A pdb=" N LEU M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.517A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 236 hydrogen bonds defined for protein. 702 hydrogen bond angles 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: 0.82 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1086 1.34 - 1.46: 576 1.46 - 1.57: 1773 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.437 0.069 3.90e-02 6.57e+02 3.09e+00 bond pdb=" CG1 ILE M 10 " pdb=" CD1 ILE M 10 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" N SER K 184 " pdb=" CA SER K 184 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.26e+00 bond pdb=" CB VAL K 118 " pdb=" CG2 VAL K 118 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.35e-02 5.49e+03 1.43e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 4325 1.34 - 2.68: 284 2.68 - 4.02: 54 4.02 - 5.36: 8 5.36 - 6.70: 3 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ILE L 103 " pdb=" CA ILE L 103 " pdb=" C ILE L 103 " ideal model delta sigma weight residual 113.42 107.77 5.65 1.17e+00 7.31e-01 2.34e+01 angle pdb=" CA ILE L 103 " pdb=" C ILE L 103 " pdb=" N GLU L 104 " ideal model delta sigma weight residual 118.90 115.40 3.50 9.40e-01 1.13e+00 1.38e+01 angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.72 115.25 5.47 1.67e+00 3.59e-01 1.07e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.83 -4.08 1.28e+00 6.10e-01 1.02e+01 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 116.19 4.49 1.70e+00 3.46e-01 6.96e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1855 16.69 - 33.37: 206 33.37 - 50.06: 40 50.06 - 66.75: 9 66.75 - 83.43: 3 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 262 0.034 - 0.067: 169 0.067 - 0.101: 58 0.101 - 0.135: 15 0.135 - 0.169: 4 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA ILE M 125 " pdb=" N ILE M 125 " pdb=" C ILE M 125 " pdb=" CB ILE M 125 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE L 103 " pdb=" N ILE L 103 " pdb=" C ILE L 103 " pdb=" CB ILE L 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB VAL K 177 " pdb=" CA VAL K 177 " pdb=" CG1 VAL K 177 " pdb=" CG2 VAL K 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 71 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ILE K 71 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE K 71 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS K 72 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 44 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO M 45 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO M 45 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 45 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 69 " 0.012 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE M 69 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE M 69 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE M 69 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE M 69 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 69 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE M 69 " 0.003 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 925 2.80 - 3.33: 3321 3.33 - 3.85: 5378 3.85 - 4.38: 5777 4.38 - 4.90: 9940 Nonbonded interactions: 25341 Sorted by model distance: nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.278 3.040 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.295 3.120 nonbonded pdb=" NH2 ARG K 143 " pdb=" O GLU L 96 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.324 3.120 nonbonded pdb=" O GLU M 35 " pdb=" OG1 THR M 38 " model vdw 2.326 3.040 ... (remaining 25336 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: 6.390 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.880 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.008 0.069 3456 Z= 0.483 Angle : 0.770 6.703 4674 Z= 0.449 Chirality : 0.048 0.169 508 Planarity : 0.005 0.042 603 Dihedral : 14.927 83.433 1299 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.39 (0.34), residues: 413 helix: -1.14 (0.25), residues: 283 sheet: None (None), residues: 0 loop : -2.34 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 103 HIS 0.003 0.001 HIS K 103 PHE 0.028 0.003 PHE M 69 TYR 0.014 0.002 TYR K 51 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.404 Fit side-chains REVERT: K 98 GLN cc_start: 0.7378 (mm110) cc_final: 0.7164 (mt0) REVERT: K 150 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6701 (mm-30) REVERT: K 165 MET cc_start: 0.7818 (tpp) cc_final: 0.7109 (mmp) REVERT: K 173 MET cc_start: 0.6700 (tpp) cc_final: 0.6448 (tpt) REVERT: L 40 GLN cc_start: 0.6025 (pt0) cc_final: 0.5796 (pt0) REVERT: L 96 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7909 (mt-10) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 1.2013 time to fit residues: 81.6559 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 115 GLN K 130 ASN K 175 ASN K 183 GLN M 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.174689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139922 restraints weight = 5040.098| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.18 r_work: 0.3565 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.226 Angle : 0.614 9.805 4674 Z= 0.331 Chirality : 0.042 0.155 508 Planarity : 0.005 0.044 603 Dihedral : 5.479 55.764 452 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.38 % Allowed : 14.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.22 (0.41), residues: 413 helix: 0.88 (0.29), residues: 287 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.011 0.002 PHE K 58 TYR 0.010 0.001 TYR K 157 ARG 0.003 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.428 Fit side-chains REVERT: K 19 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7080 (tt0) REVERT: K 98 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7108 (mt0) REVERT: K 150 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6887 (mm-30) REVERT: K 165 MET cc_start: 0.7749 (tpp) cc_final: 0.7108 (mmp) REVERT: K 175 ASN cc_start: 0.6391 (m-40) cc_final: 0.6180 (p0) REVERT: L 40 GLN cc_start: 0.5861 (pt0) cc_final: 0.5575 (pt0) REVERT: L 96 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8280 (mt-10) REVERT: M 141 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7422 (pt0) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 1.0156 time to fit residues: 66.2965 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 23 GLN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143383 restraints weight = 4977.835| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.18 r_work: 0.3595 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3456 Z= 0.167 Angle : 0.555 8.452 4674 Z= 0.300 Chirality : 0.040 0.148 508 Planarity : 0.005 0.043 603 Dihedral : 5.004 52.101 452 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.94 % Allowed : 17.46 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.15 (0.42), residues: 413 helix: 1.76 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.56 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 33 HIS 0.004 0.001 HIS K 103 PHE 0.009 0.001 PHE L 82 TYR 0.007 0.001 TYR K 157 ARG 0.004 0.001 ARG L 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.386 Fit side-chains REVERT: K 150 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6856 (mp0) REVERT: K 154 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6707 (mmm-85) REVERT: K 165 MET cc_start: 0.7734 (tpp) cc_final: 0.7087 (mmp) REVERT: L 96 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8341 (mt-10) REVERT: M 128 ASP cc_start: 0.8619 (p0) cc_final: 0.8300 (p0) outliers start: 14 outliers final: 5 residues processed: 60 average time/residue: 1.0205 time to fit residues: 63.4561 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.176818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141976 restraints weight = 5047.141| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.22 r_work: 0.3586 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.189 Angle : 0.550 9.207 4674 Z= 0.299 Chirality : 0.040 0.151 508 Planarity : 0.005 0.040 603 Dihedral : 4.934 52.531 452 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.94 % Allowed : 18.59 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.56 (0.43), residues: 413 helix: 2.05 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.011 0.001 PHE K 125 TYR 0.012 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: K 7 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: K 165 MET cc_start: 0.7738 (tpp) cc_final: 0.6905 (mmp) REVERT: L 48 ARG cc_start: 0.7470 (ppt170) cc_final: 0.7183 (ppt170) REVERT: L 96 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8371 (mt-10) REVERT: M 141 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6809 (pm20) outliers start: 14 outliers final: 4 residues processed: 60 average time/residue: 1.0763 time to fit residues: 66.8426 Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.175329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140429 restraints weight = 5023.229| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.20 r_work: 0.3564 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3456 Z= 0.240 Angle : 0.591 8.292 4674 Z= 0.316 Chirality : 0.041 0.155 508 Planarity : 0.005 0.041 603 Dihedral : 5.038 55.472 452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.79 % Allowed : 20.00 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.80 (0.43), residues: 413 helix: 2.14 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.97 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 33 HIS 0.002 0.001 HIS K 103 PHE 0.013 0.001 PHE K 125 TYR 0.010 0.001 TYR M 56 ARG 0.004 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.381 Fit side-chains REVERT: K 98 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7050 (mt0) REVERT: K 104 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7849 (mp) REVERT: K 150 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6988 (mp0) REVERT: K 154 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6765 (mmm-85) REVERT: K 164 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: K 165 MET cc_start: 0.7797 (tpp) cc_final: 0.7078 (mmp) REVERT: L 48 ARG cc_start: 0.7522 (ppt170) cc_final: 0.7229 (ppt170) REVERT: L 96 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8323 (mt-10) REVERT: M 141 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6865 (pm20) outliers start: 17 outliers final: 6 residues processed: 58 average time/residue: 1.1507 time to fit residues: 68.9481 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN M 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.177335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142642 restraints weight = 5078.625| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.21 r_work: 0.3597 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.172 Angle : 0.559 9.871 4674 Z= 0.299 Chirality : 0.039 0.150 508 Planarity : 0.005 0.040 603 Dihedral : 4.817 53.035 452 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.79 % Allowed : 20.56 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.95 (0.43), residues: 413 helix: 2.33 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.009 0.001 PHE L 82 TYR 0.008 0.001 TYR M 56 ARG 0.004 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.423 Fit side-chains REVERT: K 7 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: K 104 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7883 (mp) REVERT: K 150 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6934 (mp0) REVERT: K 154 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6768 (mmm-85) REVERT: K 165 MET cc_start: 0.7805 (tpp) cc_final: 0.7066 (mmp) REVERT: K 174 ILE cc_start: 0.4796 (tt) cc_final: 0.4055 (pp) REVERT: L 48 ARG cc_start: 0.7510 (ppt170) cc_final: 0.7228 (ppt170) REVERT: L 96 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8297 (mt-10) REVERT: M 128 ASP cc_start: 0.8621 (p0) cc_final: 0.8383 (p0) REVERT: M 141 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6825 (pm20) outliers start: 17 outliers final: 6 residues processed: 63 average time/residue: 1.1692 time to fit residues: 75.9041 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141770 restraints weight = 5019.086| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.19 r_work: 0.3580 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3456 Z= 0.211 Angle : 0.582 8.952 4674 Z= 0.306 Chirality : 0.040 0.150 508 Planarity : 0.005 0.040 603 Dihedral : 4.838 54.585 452 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.35 % Allowed : 21.69 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.91 (0.43), residues: 413 helix: 2.28 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.23 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 12 HIS 0.002 0.001 HIS K 103 PHE 0.012 0.001 PHE K 125 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.398 Fit side-chains REVERT: K 7 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: K 104 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7856 (mp) REVERT: K 150 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6932 (mp0) REVERT: K 152 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6493 (ttpt) REVERT: K 154 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6767 (mmm-85) REVERT: K 165 MET cc_start: 0.7822 (tpp) cc_final: 0.7094 (mmp) REVERT: K 174 ILE cc_start: 0.4991 (tt) cc_final: 0.4223 (pp) REVERT: L 96 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8265 (mt-10) REVERT: M 85 TYR cc_start: 0.7824 (m-80) cc_final: 0.7574 (m-80) REVERT: M 141 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6844 (pm20) outliers start: 19 outliers final: 7 residues processed: 61 average time/residue: 1.2109 time to fit residues: 76.0942 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.177170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142447 restraints weight = 4988.756| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.21 r_work: 0.3593 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3456 Z= 0.184 Angle : 0.572 10.264 4674 Z= 0.305 Chirality : 0.039 0.148 508 Planarity : 0.005 0.039 603 Dihedral : 4.743 53.139 452 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.06 (0.43), residues: 413 helix: 2.40 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.18 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 12 HIS 0.002 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.374 Fit side-chains REVERT: K 104 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7880 (mp) REVERT: K 150 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6982 (mp0) REVERT: K 152 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6526 (ttpt) REVERT: K 154 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6783 (mmm-85) REVERT: K 165 MET cc_start: 0.7813 (tpp) cc_final: 0.7030 (mmp) REVERT: K 174 ILE cc_start: 0.5041 (tt) cc_final: 0.4315 (pp) REVERT: L 48 ARG cc_start: 0.7406 (ppt170) cc_final: 0.7108 (ppt170) REVERT: L 96 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8245 (mt-10) REVERT: M 141 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6844 (pm20) outliers start: 16 outliers final: 8 residues processed: 62 average time/residue: 1.0562 time to fit residues: 67.7678 Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143228 restraints weight = 4915.790| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.21 r_work: 0.3600 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.176 Angle : 0.584 9.670 4674 Z= 0.307 Chirality : 0.039 0.158 508 Planarity : 0.005 0.040 603 Dihedral : 4.613 51.463 452 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.79 % Allowed : 22.54 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.23 (0.43), residues: 413 helix: 2.55 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.08 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE K 125 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.367 Fit side-chains REVERT: K 104 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7856 (mp) REVERT: K 150 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6964 (mp0) REVERT: K 154 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6798 (mmm-85) REVERT: K 165 MET cc_start: 0.7814 (tpp) cc_final: 0.7052 (mmp) REVERT: K 174 ILE cc_start: 0.5023 (tt) cc_final: 0.4298 (pp) REVERT: L 48 ARG cc_start: 0.7407 (ppt170) cc_final: 0.7102 (ppt170) REVERT: L 96 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8275 (mt-10) REVERT: M 141 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6836 (pm20) outliers start: 17 outliers final: 7 residues processed: 64 average time/residue: 1.1382 time to fit residues: 75.1635 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.179152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144294 restraints weight = 4934.733| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.22 r_work: 0.3622 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3456 Z= 0.160 Angle : 0.569 10.389 4674 Z= 0.298 Chirality : 0.038 0.145 508 Planarity : 0.005 0.040 603 Dihedral : 4.555 49.628 452 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.10 % Allowed : 23.66 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.36 (0.43), residues: 413 helix: 2.63 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.09 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE M 15 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.381 Fit side-chains REVERT: K 104 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (mp) REVERT: K 150 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6912 (mp0) REVERT: K 165 MET cc_start: 0.7827 (tpp) cc_final: 0.7078 (mmp) REVERT: K 174 ILE cc_start: 0.5054 (tt) cc_final: 0.4362 (pp) REVERT: L 48 ARG cc_start: 0.7398 (ppt170) cc_final: 0.7104 (ppt170) REVERT: L 96 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8276 (mt-10) REVERT: M 85 TYR cc_start: 0.7779 (m-80) cc_final: 0.7476 (m-80) REVERT: M 141 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7323 (pm20) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 1.0486 time to fit residues: 64.0991 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.179362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.144543 restraints weight = 5048.017| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.22 r_work: 0.3620 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3456 Z= 0.164 Angle : 0.572 10.106 4674 Z= 0.296 Chirality : 0.038 0.146 508 Planarity : 0.005 0.040 603 Dihedral : 4.441 48.828 452 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.10 % Allowed : 23.38 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.55 (0.43), residues: 413 helix: 2.81 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.02 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE M 15 TYR 0.007 0.001 TYR K 148 ARG 0.005 0.001 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4655.70 seconds wall clock time: 82 minutes 37.80 seconds (4957.80 seconds total)