Starting phenix.real_space_refine on Wed Mar 5 19:21:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9g_34566/03_2025/8h9g_34566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9g_34566/03_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_34566/03_2025/8h9g_34566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9g_34566/03_2025/8h9g_34566.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9g_34566/03_2025/8h9g_34566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9g_34566/03_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-5624/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: 3.78, per 1000 atoms: 1.12 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: 0.81 Conformation dependent library (CDL) restraints added in 393.8 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: 0.28 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: 0.75 Time building geometry restraints manager: 0.96 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: 5.500 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.660 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 : 0.361 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: 1.1444 time to fit residues: 77.8544 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 : 0.437 ------------------------------------------------------------------------------- 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 = 0.139920 restraints weight = 5040.102| |-----------------------------------------------------------------------------| 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: 0.7814 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 : 0.361 Fit side-chains REVERT: K 19 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7079 (tt0) REVERT: K 98 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7107 (mt0) REVERT: K 150 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6888 (mm-30) REVERT: K 165 MET cc_start: 0.7748 (tpp) cc_final: 0.7107 (mmp) REVERT: K 175 ASN cc_start: 0.6390 (m-40) cc_final: 0.6177 (p0) REVERT: L 40 GLN cc_start: 0.5866 (pt0) cc_final: 0.5579 (pt0) REVERT: L 96 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8281 (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: 0.9795 time to fit residues: 63.9338 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 : 0.349 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.176612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141851 restraints weight = 4978.755| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.18 r_work: 0.3591 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1846 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= 0.191 Angle : 0.570 8.885 4674 Z= 0.308 Chirality : 0.040 0.150 508 Planarity : 0.005 0.043 603 Dihedral : 5.108 53.549 452 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.23 % Allowed : 17.18 % 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 (0.43), residues: 413 helix: 1.71 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.38 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.004 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.007 0.001 TYR K 157 ARG 0.003 0.001 ARG K 166 *********************** 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 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.387 Fit side-chains REVERT: K 150 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6886 (mp0) REVERT: K 154 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6707 (mmm-85) REVERT: K 165 MET cc_start: 0.7723 (tpp) cc_final: 0.6925 (mmp) REVERT: L 96 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8330 (mt-10) REVERT: M 128 ASP cc_start: 0.8639 (p0) cc_final: 0.8286 (p0) outliers start: 15 outliers final: 6 residues processed: 60 average time/residue: 1.0077 time to fit residues: 62.7050 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 102 VAL 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: 0.7980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141550 restraints weight = 5051.962| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.20 r_work: 0.3580 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.199 Angle : 0.549 8.481 4674 Z= 0.298 Chirality : 0.040 0.152 508 Planarity : 0.005 0.040 603 Dihedral : 5.014 53.544 452 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.79 % Allowed : 17.75 % 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: 1.44 (0.43), residues: 413 helix: 1.97 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.44 (0.58), 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 0.006 0.001 TYR K 157 ARG 0.003 0.001 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 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: K 7 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: K 104 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (mp) REVERT: K 154 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6753 (mmm-85) REVERT: K 165 MET cc_start: 0.7737 (tpp) cc_final: 0.6884 (mmp) REVERT: L 48 ARG cc_start: 0.7489 (ppt170) cc_final: 0.7177 (ppt170) REVERT: L 96 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8372 (mt-10) REVERT: M 141 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6826 (pm20) outliers start: 17 outliers final: 6 residues processed: 63 average time/residue: 0.9470 time to fit residues: 61.8916 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 : 0.346 ------------------------------------------------------------------------------- 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 L residue 102 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.175347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140495 restraints weight = 5042.415| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.20 r_work: 0.3563 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3456 Z= 0.237 Angle : 0.585 8.334 4674 Z= 0.314 Chirality : 0.041 0.153 508 Planarity : 0.005 0.042 603 Dihedral : 5.070 55.670 452 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 19.44 % Favored : 76.06 % 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: 1.71 (0.43), residues: 413 helix: 2.10 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.002 0.001 HIS K 103 PHE 0.013 0.001 PHE K 125 TYR 0.007 0.001 TYR K 51 ARG 0.004 0.000 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 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.375 Fit side-chains REVERT: K 98 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7048 (mt0) REVERT: K 104 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7872 (mp) REVERT: K 150 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6884 (mp0) REVERT: K 154 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6777 (mmm-85) REVERT: K 165 MET cc_start: 0.7706 (tpp) cc_final: 0.7005 (mmp) REVERT: L 48 ARG cc_start: 0.7521 (ppt170) cc_final: 0.7221 (ppt170) REVERT: L 96 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8342 (mt-10) REVERT: M 141 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6859 (pm20) outliers start: 16 outliers final: 7 residues processed: 56 average time/residue: 1.0954 time to fit residues: 63.4567 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.177318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142570 restraints weight = 5099.726| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.24 r_work: 0.3595 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3456 Z= 0.172 Angle : 0.560 9.824 4674 Z= 0.300 Chirality : 0.039 0.148 508 Planarity : 0.005 0.041 603 Dihedral : 4.788 52.429 452 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 20.28 % 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: 1.99 (0.43), residues: 413 helix: 2.35 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.13 (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 0.009 0.001 PHE M 15 TYR 0.006 0.001 TYR K 157 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 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.377 Fit side-chains REVERT: K 150 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6954 (mp0) REVERT: K 154 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6815 (mmm-85) REVERT: K 165 MET cc_start: 0.7746 (tpp) cc_final: 0.7019 (mmp) REVERT: K 174 ILE cc_start: 0.4857 (tt) cc_final: 0.4138 (pp) REVERT: L 48 ARG cc_start: 0.7509 (ppt170) cc_final: 0.7227 (ppt170) REVERT: L 96 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8309 (mt-10) REVERT: M 141 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6815 (pm20) outliers start: 16 outliers final: 6 residues processed: 63 average time/residue: 1.1225 time to fit residues: 73.0491 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.176532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141813 restraints weight = 5020.682| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.19 r_work: 0.3587 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2612 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= 0.193 Angle : 0.580 9.044 4674 Z= 0.305 Chirality : 0.040 0.150 508 Planarity : 0.005 0.041 603 Dihedral : 4.804 52.956 452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.07 % Allowed : 21.13 % Favored : 73.80 % 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: 1.98 (0.43), residues: 413 helix: 2.32 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.14 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 12 HIS 0.002 0.001 HIS K 103 PHE 0.011 0.001 PHE K 125 TYR 0.015 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 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.395 Fit side-chains REVERT: K 104 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7817 (mm) REVERT: K 150 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7019 (mp0) REVERT: K 165 MET cc_start: 0.7793 (tpp) cc_final: 0.7048 (mmp) REVERT: K 174 ILE cc_start: 0.5050 (tt) cc_final: 0.4295 (pp) REVERT: L 96 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8280 (mt-10) REVERT: M 141 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6869 (pm20) outliers start: 18 outliers final: 11 residues processed: 59 average time/residue: 0.9239 time to fit residues: 56.7245 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 83 ASP 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: 0.6980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 overall best weight: 0.5440 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.178991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144335 restraints weight = 4988.331| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.23 r_work: 0.3610 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3456 Z= 0.159 Angle : 0.559 10.201 4674 Z= 0.297 Chirality : 0.039 0.146 508 Planarity : 0.005 0.039 603 Dihedral : 4.605 50.510 452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.79 % Allowed : 22.25 % 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: 2.14 (0.43), residues: 413 helix: 2.47 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 126 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 M 15 TYR 0.014 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 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.382 Fit side-chains REVERT: K 104 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (mp) REVERT: K 150 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7040 (mp0) REVERT: K 165 MET cc_start: 0.7828 (tpp) cc_final: 0.7105 (mmp) REVERT: K 174 ILE cc_start: 0.5083 (tt) cc_final: 0.4368 (pp) REVERT: L 48 ARG cc_start: 0.7420 (ppt170) cc_final: 0.7115 (ppt170) REVERT: L 96 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8266 (mt-10) REVERT: M 141 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6824 (pm20) outliers start: 17 outliers final: 8 residues processed: 63 average time/residue: 1.0379 time to fit residues: 67.6715 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 147 VAL 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: 10.0000 chunk 32 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.174581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139383 restraints weight = 4934.405| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.19 r_work: 0.3555 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3456 Z= 0.299 Angle : 0.652 9.421 4674 Z= 0.343 Chirality : 0.042 0.165 508 Planarity : 0.005 0.041 603 Dihedral : 5.032 57.960 452 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.23 % Allowed : 22.82 % 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: 2.10 (0.43), residues: 413 helix: 2.36 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.83 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 53 HIS 0.003 0.001 HIS K 172 PHE 0.017 0.002 PHE K 125 TYR 0.016 0.002 TYR M 56 ARG 0.004 0.001 ARG K 154 *********************** 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 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.369 Fit side-chains REVERT: K 7 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: K 98 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7032 (mt0) REVERT: K 104 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7843 (mp) REVERT: K 150 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6714 (mp0) REVERT: K 152 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6681 (ttpt) REVERT: K 165 MET cc_start: 0.7845 (tpp) cc_final: 0.7122 (mmp) REVERT: K 174 ILE cc_start: 0.5112 (tt) cc_final: 0.4375 (pp) REVERT: L 48 ARG cc_start: 0.7390 (ppt170) cc_final: 0.7151 (ppt170) REVERT: L 96 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8315 (mt-10) REVERT: M 141 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7054 (pm20) outliers start: 15 outliers final: 8 residues processed: 62 average time/residue: 0.9691 time to fit residues: 62.2815 Evaluate side-chains 58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 25 LEU 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 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 83 ASP 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: 2.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.176395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141391 restraints weight = 4974.749| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.20 r_work: 0.3575 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3456 Z= 0.220 Angle : 0.607 10.102 4674 Z= 0.318 Chirality : 0.040 0.159 508 Planarity : 0.005 0.041 603 Dihedral : 4.908 55.347 452 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.94 % Allowed : 23.66 % Favored : 72.39 % 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: 2.28 (0.43), residues: 413 helix: 2.51 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.81 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 53 HIS 0.002 0.001 HIS K 103 PHE 0.011 0.001 PHE K 125 TYR 0.014 0.001 TYR M 56 ARG 0.004 0.001 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 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.355 Fit side-chains REVERT: K 98 GLN cc_start: 0.7633 (mm-40) cc_final: 0.6990 (mt0) REVERT: K 104 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7848 (mp) REVERT: K 150 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7056 (mp0) REVERT: K 152 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6552 (ttpt) REVERT: K 165 MET cc_start: 0.7817 (tpp) cc_final: 0.7042 (mmp) REVERT: K 174 ILE cc_start: 0.5260 (tt) cc_final: 0.4569 (pp) REVERT: L 48 ARG cc_start: 0.7435 (ppt170) cc_final: 0.7124 (ppt170) REVERT: L 96 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8301 (mt-10) REVERT: M 85 TYR cc_start: 0.7855 (m-80) cc_final: 0.7585 (m-80) REVERT: M 141 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6888 (pm20) outliers start: 14 outliers final: 6 residues processed: 59 average time/residue: 1.0617 time to fit residues: 64.8310 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain K residue 152 LYS 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: 2.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 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: 0.8980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.177605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142569 restraints weight = 5056.231| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.23 r_work: 0.3599 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3456 Z= 0.184 Angle : 0.610 10.025 4674 Z= 0.314 Chirality : 0.040 0.158 508 Planarity : 0.005 0.041 603 Dihedral : 4.699 52.361 452 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.38 % Allowed : 24.23 % Favored : 72.39 % 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: 2.38 (0.43), residues: 413 helix: 2.64 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -0.97 (0.61), residues: 129 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 0.013 0.001 TYR M 56 ARG 0.004 0.001 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4512.42 seconds wall clock time: 77 minutes 32.01 seconds (4652.01 seconds total)