Starting phenix.real_space_refine on Thu Mar 6 02:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.map" model { file = "/net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iep_35389/03_2025/8iep_35389.cif" } resolution = 2.61 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 2939 2.51 5 N 695 2.21 5 O 759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 4431 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2155 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2172 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 8, 'TRANS': 270} Chain breaks: 2 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.10, per 1000 atoms: 0.93 Number of scatterers: 4431 At special positions: 0 Unit cell: (76.95, 85.86, 102.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 759 8.00 N 695 7.00 C 2939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 216 " distance=2.03 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: 1.44 Conformation dependent library (CDL) restraints added in 542.7 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 1 sheets defined 79.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.671A pdb=" N ILE C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 150 Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 161 through 187 removed outlier: 3.599A pdb=" N LEU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 246 removed outlier: 4.089A pdb=" N TRP C 224 " --> pdb=" O TYR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 281 Processing helix chain 'C' and resid 284 through 332 Proline residue: C 310 - end of helix Processing helix chain 'D' and resid 46 through 74 Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.595A pdb=" N VAL D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 149 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 162 through 187 removed outlier: 3.558A pdb=" N ASP D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 246 removed outlier: 3.539A pdb=" N TRP D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 281 Processing helix chain 'D' and resid 284 through 332 Proline residue: D 310 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 206 through 216 removed outlier: 3.604A pdb=" N PHE C 215 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU C 195 " --> pdb=" O MET D 199 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1152 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: 1.21 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 637 1.31 - 1.44: 1216 1.44 - 1.56: 2604 1.56 - 1.69: 12 1.69 - 1.81: 52 Bond restraints: 4521 Sorted by residual: bond pdb=" C39 PC1 C 601 " pdb=" C3A PC1 C 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C39 PC1 D 601 " pdb=" C3A PC1 D 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C31 PC1 D 601 " pdb=" O31 PC1 D 601 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 PC1 C 601 " pdb=" O31 PC1 C 601 " ideal model delta sigma weight residual 1.330 1.425 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C21 PC1 D 601 " pdb=" O21 PC1 D 601 " ideal model delta sigma weight residual 1.331 1.383 -0.052 2.00e-02 2.50e+03 6.68e+00 ... (remaining 4516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 6055 2.81 - 5.62: 64 5.62 - 8.43: 10 8.43 - 11.24: 0 11.24 - 14.05: 2 Bond angle restraints: 6131 Sorted by residual: angle pdb=" O12 PC1 C 601 " pdb=" P PC1 C 601 " pdb=" O14 PC1 C 601 " ideal model delta sigma weight residual 123.67 109.62 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O12 PC1 D 601 " pdb=" P PC1 D 601 " pdb=" O14 PC1 D 601 " ideal model delta sigma weight residual 123.67 109.68 13.99 3.00e+00 1.11e-01 2.18e+01 angle pdb=" CB TRP D 229 " pdb=" CG TRP D 229 " pdb=" CD2 TRP D 229 " ideal model delta sigma weight residual 126.80 131.54 -4.74 1.40e+00 5.10e-01 1.14e+01 angle pdb=" CB TRP C 229 " pdb=" CG TRP C 229 " pdb=" CD2 TRP C 229 " ideal model delta sigma weight residual 126.80 131.38 -4.58 1.40e+00 5.10e-01 1.07e+01 angle pdb=" CB TRP D 229 " pdb=" CG TRP D 229 " pdb=" CD1 TRP D 229 " ideal model delta sigma weight residual 126.90 122.53 4.37 1.50e+00 4.44e-01 8.47e+00 ... (remaining 6126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2430 17.93 - 35.87: 193 35.87 - 53.80: 39 53.80 - 71.74: 4 71.74 - 89.67: 7 Dihedral angle restraints: 2673 sinusoidal: 1068 harmonic: 1605 Sorted by residual: dihedral pdb=" CA ILE D 228 " pdb=" C ILE D 228 " pdb=" N TRP D 229 " pdb=" CA TRP D 229 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ILE D 307 " pdb=" C ILE D 307 " pdb=" N PHE D 308 " pdb=" CA PHE D 308 " ideal model delta harmonic sigma weight residual 180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ILE C 307 " pdb=" C ILE C 307 " pdb=" N PHE C 308 " pdb=" CA PHE C 308 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 2670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 585 0.044 - 0.088: 132 0.088 - 0.132: 32 0.132 - 0.176: 1 0.176 - 0.219: 2 Chirality restraints: 752 Sorted by residual: chirality pdb=" CA TRP C 229 " pdb=" N TRP C 229 " pdb=" C TRP C 229 " pdb=" CB TRP C 229 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TRP D 229 " pdb=" N TRP D 229 " pdb=" C TRP D 229 " pdb=" CB TRP D 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CB ILE D 225 " pdb=" CA ILE D 225 " pdb=" CG1 ILE D 225 " pdb=" CG2 ILE D 225 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 749 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 229 " 0.026 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP D 229 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 229 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 229 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 229 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 229 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 229 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 229 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 229 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 229 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 229 " -0.024 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP C 229 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP C 229 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 229 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 229 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 229 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 229 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 229 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 229 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 252 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 253 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " -0.043 5.00e-02 4.00e+02 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 96 2.71 - 3.26: 4336 3.26 - 3.80: 7128 3.80 - 4.35: 8488 4.35 - 4.90: 15329 Nonbonded interactions: 35377 Sorted by model distance: nonbonded pdb=" OG SER C 58 " pdb=" OH TYR C 103 " model vdw 2.159 3.040 nonbonded pdb=" O TYR D 146 " pdb=" OG1 THR D 150 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR C 202 " pdb=" OD1 ASP C 205 " model vdw 2.189 3.040 nonbonded pdb=" OG SER D 95 " pdb=" OD1 ASN D 304 " model vdw 2.266 3.040 nonbonded pdb=" O TYR C 146 " pdb=" OG1 THR C 150 " model vdw 2.284 3.040 ... (remaining 35372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 44 through 152 or resid 161 through 332 or resid 601)) selection = (chain 'D' and (resid 44 through 110 or resid 115 through 151 or (resid 152 thro \ ugh 161 and (name N or name CA or name C or name O or name CB )) or resid 162 th \ rough 332 or resid 601)) } 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: 16.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 0.197 4521 Z= 0.503 Angle : 0.785 14.045 6131 Z= 0.379 Chirality : 0.040 0.219 752 Planarity : 0.006 0.077 712 Dihedral : 14.244 89.673 1629 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.35), residues: 545 helix: 2.79 (0.23), residues: 425 sheet: 1.91 (0.98), residues: 34 loop : -2.26 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP D 229 HIS 0.002 0.000 HIS C 73 PHE 0.007 0.001 PHE D 67 TYR 0.009 0.001 TYR C 280 ARG 0.002 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.620 Fit side-chains REVERT: C 82 MET cc_start: 0.7989 (ptt) cc_final: 0.7728 (ptp) REVERT: C 115 SER cc_start: 0.8315 (m) cc_final: 0.8095 (t) REVERT: C 149 PHE cc_start: 0.6381 (t80) cc_final: 0.6156 (t80) REVERT: C 199 MET cc_start: 0.6610 (ttt) cc_final: 0.6288 (ttt) REVERT: D 199 MET cc_start: 0.6786 (mtp) cc_final: 0.6538 (mtp) REVERT: D 235 LEU cc_start: 0.7958 (mm) cc_final: 0.7755 (tp) REVERT: D 283 SER cc_start: 0.8188 (m) cc_final: 0.7929 (p) REVERT: D 318 PHE cc_start: 0.6959 (t80) cc_final: 0.6728 (t80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.5624 time to fit residues: 53.5042 Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN D 282 HIS D 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113341 restraints weight = 5761.660| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.73 r_work: 0.3432 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4521 Z= 0.266 Angle : 0.549 6.846 6131 Z= 0.293 Chirality : 0.041 0.192 752 Planarity : 0.006 0.067 712 Dihedral : 11.173 81.111 676 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.85 % Allowed : 6.92 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.34), residues: 545 helix: 3.10 (0.22), residues: 427 sheet: 2.38 (0.95), residues: 34 loop : -1.91 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 229 HIS 0.001 0.000 HIS D 73 PHE 0.012 0.001 PHE D 318 TYR 0.012 0.001 TYR D 103 ARG 0.002 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.450 Fit side-chains REVERT: C 107 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7380 (mt) REVERT: D 279 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8486 (ttm170) outliers start: 14 outliers final: 3 residues processed: 75 average time/residue: 0.5976 time to fit residues: 48.2269 Evaluate side-chains 71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.0040 chunk 30 optimal weight: 0.0980 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 36 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.0688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115750 restraints weight = 5823.004| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.75 r_work: 0.3474 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4521 Z= 0.124 Angle : 0.466 7.833 6131 Z= 0.248 Chirality : 0.036 0.172 752 Planarity : 0.005 0.069 712 Dihedral : 10.128 76.110 676 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.24 % Allowed : 7.74 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.34), residues: 545 helix: 3.40 (0.22), residues: 428 sheet: 2.74 (1.42), residues: 14 loop : -1.23 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 229 HIS 0.001 0.000 HIS C 214 PHE 0.004 0.001 PHE C 289 TYR 0.008 0.001 TYR D 103 ARG 0.002 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.630 Fit side-chains REVERT: C 107 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7331 (mt) REVERT: D 279 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8394 (ttm170) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 1.2225 time to fit residues: 91.6300 Evaluate side-chains 71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 overall best weight: 0.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115093 restraints weight = 5754.441| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.73 r_work: 0.3448 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4521 Z= 0.146 Angle : 0.469 7.389 6131 Z= 0.249 Chirality : 0.037 0.182 752 Planarity : 0.005 0.070 712 Dihedral : 10.281 83.561 676 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.44 % Allowed : 9.57 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.34), residues: 545 helix: 3.54 (0.22), residues: 429 sheet: 2.90 (1.43), residues: 14 loop : -1.17 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.007 0.001 PHE D 70 TYR 0.010 0.001 TYR D 103 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.630 Fit side-chains REVERT: C 107 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7338 (mt) REVERT: C 209 THR cc_start: 0.8329 (m) cc_final: 0.7967 (t) REVERT: D 116 MET cc_start: 0.8337 (mmm) cc_final: 0.8134 (mmm) REVERT: D 279 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8451 (ttm170) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 1.1493 time to fit residues: 80.6875 Evaluate side-chains 69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113986 restraints weight = 5868.857| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.73 r_work: 0.3446 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4521 Z= 0.192 Angle : 0.487 7.879 6131 Z= 0.257 Chirality : 0.039 0.193 752 Planarity : 0.005 0.070 712 Dihedral : 10.552 84.842 676 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.24 % Allowed : 10.39 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.34), residues: 545 helix: 3.53 (0.22), residues: 429 sheet: 2.81 (1.42), residues: 14 loop : -1.17 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.009 0.001 PHE D 318 TYR 0.009 0.001 TYR D 103 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.509 Fit side-chains REVERT: C 107 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7385 (mt) REVERT: D 279 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8478 (ttm170) outliers start: 11 outliers final: 5 residues processed: 74 average time/residue: 0.6133 time to fit residues: 48.8153 Evaluate side-chains 71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113651 restraints weight = 5743.338| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.72 r_work: 0.3426 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4521 Z= 0.199 Angle : 0.499 8.514 6131 Z= 0.263 Chirality : 0.039 0.197 752 Planarity : 0.005 0.071 712 Dihedral : 10.907 87.779 676 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.44 % Allowed : 12.22 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.34), residues: 545 helix: 3.47 (0.22), residues: 430 sheet: 2.72 (0.90), residues: 34 loop : -1.38 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.012 0.001 PHE C 275 TYR 0.009 0.001 TYR C 280 ARG 0.002 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.516 Fit side-chains REVERT: C 107 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7410 (mt) REVERT: C 319 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: D 279 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8405 (ttm170) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.7994 time to fit residues: 60.7872 Evaluate side-chains 71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112670 restraints weight = 5761.430| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.72 r_work: 0.3412 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4521 Z= 0.259 Angle : 0.538 8.426 6131 Z= 0.281 Chirality : 0.041 0.207 752 Planarity : 0.005 0.070 712 Dihedral : 11.251 88.554 676 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 12.22 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.34), residues: 545 helix: 3.37 (0.22), residues: 431 sheet: 2.79 (0.90), residues: 34 loop : -1.38 (0.69), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.014 0.002 PHE D 318 TYR 0.010 0.001 TYR C 146 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.457 Fit side-chains REVERT: C 107 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7464 (mt) REVERT: C 148 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8533 (m) REVERT: C 319 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: D 279 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8543 (ttt90) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.6247 time to fit residues: 48.9387 Evaluate side-chains 73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 23 optimal weight: 0.1980 chunk 52 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113699 restraints weight = 5699.788| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.71 r_work: 0.3429 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4521 Z= 0.185 Angle : 0.520 9.093 6131 Z= 0.268 Chirality : 0.039 0.204 752 Planarity : 0.005 0.069 712 Dihedral : 11.234 87.329 676 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.83 % Allowed : 13.24 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.34), residues: 545 helix: 3.44 (0.22), residues: 430 sheet: 2.67 (0.88), residues: 34 loop : -1.36 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.013 0.001 PHE C 275 TYR 0.009 0.001 TYR D 103 ARG 0.003 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.452 Fit side-chains REVERT: C 319 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: D 279 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8421 (ttm170) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.7042 time to fit residues: 50.3329 Evaluate side-chains 71 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111527 restraints weight = 5769.413| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.70 r_work: 0.3395 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4521 Z= 0.344 Angle : 0.618 12.697 6131 Z= 0.311 Chirality : 0.044 0.214 752 Planarity : 0.006 0.072 712 Dihedral : 11.567 81.424 676 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.04 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.34), residues: 545 helix: 3.20 (0.22), residues: 432 sheet: 2.64 (0.87), residues: 34 loop : -1.38 (0.70), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 284 HIS 0.001 0.000 HIS C 248 PHE 0.017 0.002 PHE C 275 TYR 0.012 0.001 TYR C 146 ARG 0.002 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.448 Fit side-chains REVERT: C 56 PHE cc_start: 0.8143 (m-80) cc_final: 0.7605 (m-80) REVERT: C 148 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8551 (m) REVERT: C 149 PHE cc_start: 0.7274 (t80) cc_final: 0.6951 (t80) REVERT: C 319 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: C 326 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6859 (mmm-85) REVERT: D 279 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8552 (ttm170) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 0.7513 time to fit residues: 52.8290 Evaluate side-chains 69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113550 restraints weight = 5706.045| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.68 r_work: 0.3430 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4521 Z= 0.192 Angle : 0.563 14.312 6131 Z= 0.280 Chirality : 0.039 0.209 752 Planarity : 0.005 0.069 712 Dihedral : 11.298 83.242 676 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.83 % Allowed : 14.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.34), residues: 545 helix: 3.38 (0.22), residues: 430 sheet: 2.63 (0.87), residues: 34 loop : -1.37 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 315 HIS 0.001 0.000 HIS D 214 PHE 0.015 0.001 PHE C 275 TYR 0.009 0.001 TYR D 103 ARG 0.003 0.000 ARG C 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.438 Fit side-chains REVERT: C 56 PHE cc_start: 0.8133 (m-80) cc_final: 0.7586 (m-80) REVERT: C 149 PHE cc_start: 0.7251 (t80) cc_final: 0.6929 (t80) REVERT: C 319 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: D 279 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8392 (ttm170) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.7131 time to fit residues: 50.9190 Evaluate side-chains 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 47 optimal weight: 0.0670 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113897 restraints weight = 5763.186| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.70 r_work: 0.3429 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4521 Z= 0.194 Angle : 0.529 9.782 6131 Z= 0.272 Chirality : 0.039 0.208 752 Planarity : 0.005 0.069 712 Dihedral : 11.199 82.385 676 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.22 % Allowed : 14.87 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.34), residues: 545 helix: 3.40 (0.22), residues: 430 sheet: 2.60 (0.87), residues: 34 loop : -1.31 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.014 0.001 PHE C 275 TYR 0.009 0.001 TYR D 103 ARG 0.003 0.000 ARG C 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.73 seconds wall clock time: 67 minutes 49.13 seconds (4069.13 seconds total)