Starting phenix.real_space_refine on Tue Feb 11 00:20:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9n_34574/02_2025/8h9n_34574.cif" } resolution = 3.56 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= 0.011 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 29 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: 4.59, per 1000 atoms: 1.36 Number of scatterers: 3381 At special positions: 0 Unit cell: (81.03, 96.36, 207.32, 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: 0.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.22 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: 3.900A 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: 3.789A 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: 4.318A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.690A 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: 3.896A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.690A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.662A 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 13 237 hydrogen bonds defined for protein. 705 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: 0.76 Time building geometry restraints manager: 0.88 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: 1078 1.34 - 1.45: 470 1.45 - 1.57: 1887 1.57 - 1.69: 0 1.69 - 1.80: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N LEU M 76 " pdb=" CA LEU M 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS K 168 " pdb=" CA LYS K 168 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.89e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.441 0.065 3.90e-02 6.57e+02 2.79e+00 bond pdb=" CB THR K 139 " pdb=" CG2 THR K 139 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4467 1.92 - 3.84: 185 3.84 - 5.77: 19 5.77 - 7.69: 2 7.69 - 9.61: 1 Bond angle restraints: 4674 Sorted by residual: angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.31 114.62 5.69 1.52e+00 4.33e-01 1.40e+01 angle pdb=" C LYS K 72 " pdb=" N LYS K 73 " pdb=" CA LYS K 73 " ideal model delta sigma weight residual 121.80 114.95 6.85 2.16e+00 2.14e-01 1.01e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.44 -3.69 1.28e+00 6.10e-01 8.31e+00 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.24e+00 angle pdb=" CA LEU K 117 " pdb=" CB LEU K 117 " pdb=" CG LEU K 117 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1847 16.70 - 33.39: 210 33.39 - 50.09: 40 50.09 - 66.79: 12 66.79 - 83.49: 4 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 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+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 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+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 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 220 0.029 - 0.058: 170 0.058 - 0.087: 67 0.087 - 0.116: 31 0.116 - 0.145: 20 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA VAL M 80 " pdb=" N VAL M 80 " pdb=" C VAL M 80 " pdb=" CB VAL M 80 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA PHE K 58 " pdb=" N PHE K 58 " pdb=" C PHE K 58 " pdb=" CB PHE K 58 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO K 76 " pdb=" N PRO K 76 " pdb=" C PRO K 76 " pdb=" CB PRO K 76 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M 69 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE M 69 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE M 69 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU M 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE K 159 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE K 159 " -0.011 2.00e-02 2.50e+03 pdb=" N SER K 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 139 " 0.014 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE M 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE M 139 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE M 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE M 139 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE M 139 " 0.002 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 295 2.72 - 3.27: 3535 3.27 - 3.81: 5368 3.81 - 4.36: 5909 4.36 - 4.90: 10125 Nonbonded interactions: 25232 Sorted by model distance: nonbonded pdb=" O VAL K 181 " pdb=" OG SER K 184 " model vdw 2.178 3.040 nonbonded pdb=" NZ LYS K 84 " pdb=" OE1 GLU K 87 " model vdw 2.254 3.120 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP K 126 " pdb=" NH2 ARG K 129 " model vdw 2.278 3.120 ... (remaining 25227 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.007 0.065 3456 Z= 0.443 Angle : 0.878 9.610 4674 Z= 0.496 Chirality : 0.052 0.145 508 Planarity : 0.006 0.040 603 Dihedral : 15.253 83.485 1299 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -2.28 (0.34), residues: 413 helix: -1.09 (0.25), residues: 285 sheet: None (None), residues: 0 loop : -2.19 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 176 HIS 0.006 0.003 HIS K 158 PHE 0.030 0.003 PHE M 139 TYR 0.020 0.003 TYR K 140 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 117 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 56 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7139 (tt0) REVERT: K 154 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7256 (mtp180) REVERT: K 169 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8248 (tp30) REVERT: L 47 ILE cc_start: 0.8384 (pt) cc_final: 0.7695 (pt) REVERT: L 91 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7350 (Cg_exo) REVERT: L 103 ILE cc_start: 0.5678 (mt) cc_final: 0.5461 (mt) REVERT: L 105 LYS cc_start: 0.5593 (tmtt) cc_final: 0.5125 (tptt) REVERT: M 96 ASP cc_start: 0.8088 (t0) cc_final: 0.7866 (t70) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2226 time to fit residues: 29.7612 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 103 HIS K 115 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 GLN M 23 GLN M 47 ASN M 59 ASN M 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.135389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117098 restraints weight = 8189.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118407 restraints weight = 4531.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.118744 restraints weight = 3524.072| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3456 Z= 0.256 Angle : 0.640 7.541 4674 Z= 0.347 Chirality : 0.042 0.147 508 Planarity : 0.006 0.047 603 Dihedral : 5.160 45.435 452 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.23 % Allowed : 14.93 % Favored : 80.85 % 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: 0.40 (0.41), residues: 413 helix: 1.15 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.004 0.002 HIS K 158 PHE 0.018 0.002 PHE L 93 TYR 0.019 0.002 TYR M 56 ARG 0.006 0.001 ARG M 40 *********************** 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 102 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: K 154 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.6979 (ttm170) REVERT: L 47 ILE cc_start: 0.8213 (pt) cc_final: 0.7617 (pt) REVERT: L 103 ILE cc_start: 0.5920 (mt) cc_final: 0.5501 (mt) REVERT: M 96 ASP cc_start: 0.7969 (t0) cc_final: 0.7756 (t70) REVERT: M 119 GLU cc_start: 0.6584 (tp30) cc_final: 0.6362 (tp30) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.1865 time to fit residues: 20.6659 Evaluate side-chains 83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119171 restraints weight = 8107.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.119657 restraints weight = 3741.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120629 restraints weight = 2491.889| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3456 Z= 0.170 Angle : 0.575 7.252 4674 Z= 0.309 Chirality : 0.039 0.140 508 Planarity : 0.005 0.042 603 Dihedral : 4.770 39.226 452 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.66 % Allowed : 19.15 % Favored : 77.18 % 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: 1.49 (0.43), residues: 413 helix: 2.01 (0.31), residues: 285 sheet: None (None), residues: 0 loop : -1.45 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.002 0.001 HIS K 158 PHE 0.022 0.002 PHE K 24 TYR 0.018 0.002 TYR K 74 ARG 0.006 0.001 ARG K 167 *********************** 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 95 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: K 169 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8301 (tp30) REVERT: K 178 GLU cc_start: 0.8077 (mm-30) cc_final: 0.6917 (tm-30) REVERT: L 47 ILE cc_start: 0.8271 (pt) cc_final: 0.7734 (pt) REVERT: M 92 GLU cc_start: 0.6851 (tp30) cc_final: 0.6513 (tp30) REVERT: M 96 ASP cc_start: 0.7906 (t0) cc_final: 0.7652 (t70) REVERT: M 119 GLU cc_start: 0.6478 (tp30) cc_final: 0.6271 (tp30) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.1878 time to fit residues: 19.6742 Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 169 GLU Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 93 GLU 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: 5.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.118051 restraints weight = 8235.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.119558 restraints weight = 4004.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120204 restraints weight = 2414.362| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3456 Z= 0.184 Angle : 0.570 5.473 4674 Z= 0.311 Chirality : 0.040 0.189 508 Planarity : 0.005 0.043 603 Dihedral : 4.519 31.657 452 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.23 % Allowed : 20.00 % Favored : 75.77 % 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: 1.88 (0.42), residues: 413 helix: 2.34 (0.30), residues: 279 sheet: None (None), residues: 0 loop : -1.23 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 53 HIS 0.002 0.001 HIS K 158 PHE 0.028 0.002 PHE K 24 TYR 0.011 0.001 TYR M 85 ARG 0.005 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 90 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.379 Fit side-chains REVERT: K 150 GLU cc_start: 0.7404 (tp30) cc_final: 0.7172 (tp30) REVERT: K 164 MET cc_start: 0.8322 (tpt) cc_final: 0.7660 (tpt) REVERT: K 165 MET cc_start: 0.8239 (mtp) cc_final: 0.6938 (tmm) REVERT: K 178 GLU cc_start: 0.7978 (mm-30) cc_final: 0.6900 (tm-30) REVERT: L 47 ILE cc_start: 0.8236 (pt) cc_final: 0.7760 (pt) REVERT: L 81 MET cc_start: 0.8053 (ppp) cc_final: 0.7810 (ppp) REVERT: M 92 GLU cc_start: 0.6961 (tp30) cc_final: 0.6621 (tp30) REVERT: M 96 ASP cc_start: 0.7831 (t0) cc_final: 0.7567 (t70) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.1808 time to fit residues: 18.1432 Evaluate side-chains 79 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 23 GLN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116081 restraints weight = 8212.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118301 restraints weight = 3790.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119604 restraints weight = 2250.613| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3821 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= 0.165 Angle : 0.573 6.396 4674 Z= 0.311 Chirality : 0.041 0.215 508 Planarity : 0.005 0.041 603 Dihedral : 4.430 26.558 452 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.51 % Allowed : 18.59 % Favored : 76.90 % 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: 2.04 (0.42), residues: 413 helix: 2.40 (0.30), residues: 279 sheet: None (None), residues: 0 loop : -1.00 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 53 HIS 0.002 0.001 HIS K 180 PHE 0.021 0.002 PHE K 24 TYR 0.025 0.002 TYR M 85 ARG 0.005 0.001 ARG K 154 *********************** 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 91 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.398 Fit side-chains REVERT: K 148 TYR cc_start: 0.7662 (t80) cc_final: 0.7416 (t80) REVERT: L 47 ILE cc_start: 0.8217 (pt) cc_final: 0.7770 (pt) REVERT: M 92 GLU cc_start: 0.6925 (tp30) cc_final: 0.6570 (tp30) REVERT: M 96 ASP cc_start: 0.7839 (t0) cc_final: 0.7596 (t70) REVERT: M 119 GLU cc_start: 0.6520 (tp30) cc_final: 0.6313 (tp30) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.2070 time to fit residues: 20.1060 Evaluate side-chains 80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.0470 chunk 35 optimal weight: 8.9990 chunk 25 optimal weight: 0.0270 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.137833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.119659 restraints weight = 8440.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121469 restraints weight = 4884.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121521 restraints weight = 3490.607| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3456 Z= 0.174 Angle : 0.583 7.496 4674 Z= 0.313 Chirality : 0.040 0.166 508 Planarity : 0.005 0.059 603 Dihedral : 4.267 21.593 452 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.23 % Allowed : 19.44 % Favored : 76.34 % 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: 2.34 (0.42), residues: 413 helix: 2.59 (0.29), residues: 284 sheet: None (None), residues: 0 loop : -0.92 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 53 HIS 0.004 0.001 HIS K 180 PHE 0.010 0.001 PHE L 100 TYR 0.023 0.001 TYR M 85 ARG 0.007 0.001 ARG K 141 *********************** 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 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.309 Fit side-chains REVERT: K 120 LYS cc_start: 0.8732 (tppt) cc_final: 0.8227 (ttpt) REVERT: K 137 GLU cc_start: 0.8046 (tp30) cc_final: 0.7585 (tp30) REVERT: K 141 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8097 (mtm-85) REVERT: L 47 ILE cc_start: 0.8201 (pt) cc_final: 0.7781 (pt) REVERT: L 81 MET cc_start: 0.8281 (ppp) cc_final: 0.7934 (tmm) REVERT: M 92 GLU cc_start: 0.6891 (tp30) cc_final: 0.6530 (tp30) REVERT: M 96 ASP cc_start: 0.7896 (t0) cc_final: 0.7646 (t70) REVERT: M 157 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7040 (mp) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.2073 time to fit residues: 19.2074 Evaluate side-chains 80 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 0.0060 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.137434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118406 restraints weight = 8321.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119544 restraints weight = 4449.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120683 restraints weight = 2493.335| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3456 Z= 0.185 Angle : 0.602 6.775 4674 Z= 0.322 Chirality : 0.041 0.145 508 Planarity : 0.005 0.040 603 Dihedral : 4.178 18.474 452 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: 2.37 (0.42), residues: 413 helix: 2.56 (0.29), residues: 285 sheet: None (None), residues: 0 loop : -0.81 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 53 HIS 0.002 0.001 HIS K 180 PHE 0.020 0.002 PHE K 24 TYR 0.023 0.002 TYR K 148 ARG 0.004 0.001 ARG K 167 *********************** 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 89 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.378 Fit side-chains REVERT: K 120 LYS cc_start: 0.8730 (tppt) cc_final: 0.8163 (ttpt) REVERT: K 137 GLU cc_start: 0.7911 (tp30) cc_final: 0.7402 (tp30) REVERT: K 141 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: L 47 ILE cc_start: 0.8227 (pt) cc_final: 0.7925 (pt) REVERT: L 101 GLU cc_start: 0.5616 (mp0) cc_final: 0.5286 (mp0) REVERT: M 92 GLU cc_start: 0.6943 (tp30) cc_final: 0.6577 (tp30) REVERT: M 96 ASP cc_start: 0.7887 (t0) cc_final: 0.7625 (t70) REVERT: M 157 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7050 (mp) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.2047 time to fit residues: 19.1001 Evaluate side-chains 82 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE 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: 4.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119752 restraints weight = 8253.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.121194 restraints weight = 4854.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121485 restraints weight = 3555.111| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3456 Z= 0.183 Angle : 0.602 6.451 4674 Z= 0.323 Chirality : 0.040 0.137 508 Planarity : 0.005 0.040 603 Dihedral : 4.122 18.661 452 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.23 % Allowed : 20.28 % Favored : 75.49 % 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: 2.47 (0.42), residues: 413 helix: 2.63 (0.29), residues: 285 sheet: None (None), residues: 0 loop : -0.73 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 176 HIS 0.003 0.001 HIS K 180 PHE 0.010 0.001 PHE L 100 TYR 0.023 0.002 TYR M 85 ARG 0.004 0.001 ARG K 167 *********************** 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 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.407 Fit side-chains REVERT: K 120 LYS cc_start: 0.8761 (tppt) cc_final: 0.8271 (ttpt) REVERT: K 137 GLU cc_start: 0.7895 (tp30) cc_final: 0.7485 (tp30) REVERT: K 141 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8329 (mtm-85) REVERT: K 165 MET cc_start: 0.8269 (mtp) cc_final: 0.6996 (tmm) REVERT: L 47 ILE cc_start: 0.8171 (pt) cc_final: 0.7945 (pt) REVERT: L 55 GLN cc_start: 0.7714 (pp30) cc_final: 0.7408 (pp30) REVERT: M 92 GLU cc_start: 0.6878 (tp30) cc_final: 0.6513 (tp30) REVERT: M 96 ASP cc_start: 0.7935 (t0) cc_final: 0.7575 (t0) REVERT: M 157 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7003 (mp) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.1908 time to fit residues: 17.7805 Evaluate side-chains 77 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 130 ASN K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119161 restraints weight = 8140.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120853 restraints weight = 4739.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.120905 restraints weight = 3468.651| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3456 Z= 0.203 Angle : 0.626 6.058 4674 Z= 0.335 Chirality : 0.041 0.138 508 Planarity : 0.005 0.041 603 Dihedral : 4.103 19.013 452 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.94 % Allowed : 20.85 % 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: 2.43 (0.42), residues: 413 helix: 2.64 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.74 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 176 HIS 0.002 0.001 HIS K 172 PHE 0.021 0.002 PHE K 24 TYR 0.024 0.002 TYR M 85 ARG 0.009 0.001 ARG L 48 *********************** 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 83 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: K 120 LYS cc_start: 0.8763 (tppt) cc_final: 0.8129 (ttpt) REVERT: K 137 GLU cc_start: 0.7899 (tp30) cc_final: 0.7427 (tp30) REVERT: K 141 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8307 (mtm-85) REVERT: K 165 MET cc_start: 0.8271 (mtp) cc_final: 0.7035 (tmm) REVERT: L 86 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7404 (p0) REVERT: M 92 GLU cc_start: 0.6912 (tp30) cc_final: 0.6529 (tp30) REVERT: M 157 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.6941 (mp) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 0.2056 time to fit residues: 18.5213 Evaluate side-chains 76 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119131 restraints weight = 8156.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.120531 restraints weight = 4313.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121860 restraints weight = 2151.194| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4670 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= 0.193 Angle : 0.668 9.809 4674 Z= 0.356 Chirality : 0.041 0.137 508 Planarity : 0.005 0.040 603 Dihedral : 4.099 18.319 452 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: 2.51 (0.42), residues: 413 helix: 2.65 (0.29), residues: 285 sheet: None (None), residues: 0 loop : -0.71 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 176 HIS 0.011 0.002 HIS K 180 PHE 0.013 0.001 PHE K 125 TYR 0.024 0.001 TYR M 85 ARG 0.007 0.001 ARG M 40 ********************** 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 81 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.410 Fit side-chains REVERT: K 120 LYS cc_start: 0.8731 (tppt) cc_final: 0.8081 (ttpt) REVERT: K 137 GLU cc_start: 0.7871 (tp30) cc_final: 0.7285 (tp30) REVERT: K 141 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8283 (mtm-85) REVERT: K 148 TYR cc_start: 0.7414 (t80) cc_final: 0.7197 (t80) REVERT: K 150 GLU cc_start: 0.7323 (tp30) cc_final: 0.7016 (tp30) REVERT: M 92 GLU cc_start: 0.6834 (tp30) cc_final: 0.6487 (tp30) REVERT: M 157 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6863 (mt) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.1867 time to fit residues: 16.6487 Evaluate side-chains 75 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 180 HIS Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 157 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 180 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.138224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.119852 restraints weight = 8365.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121661 restraints weight = 4840.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121681 restraints weight = 3498.431| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4728 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= 0.200 Angle : 0.670 7.898 4674 Z= 0.358 Chirality : 0.041 0.144 508 Planarity : 0.005 0.040 603 Dihedral : 4.099 18.716 452 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.10 % Allowed : 23.94 % 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: 2.42 (0.42), residues: 413 helix: 2.66 (0.30), residues: 280 sheet: None (None), residues: 0 loop : -0.80 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 12 HIS 0.007 0.001 HIS K 180 PHE 0.021 0.001 PHE K 24 TYR 0.024 0.001 TYR M 85 ARG 0.007 0.001 ARG M 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.64 seconds wall clock time: 36 minutes 8.70 seconds (2168.70 seconds total)