Starting phenix.real_space_refine on Sat May 10 01:18:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.map" model { file = "/net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iei_35382/05_2025/8iei_35382.cif" } resolution = 2.62 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 2961 2.51 5 N 704 2.21 5 O 767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4469 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2135 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 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: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2230 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "A" 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: "B" 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: 4.28, per 1000 atoms: 0.96 Number of scatterers: 4469 At special positions: 0 Unit cell: (68.04, 89.1, 102.87, 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 35 16.00 P 2 15.00 O 767 8.00 N 704 7.00 C 2961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 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: 1.12 Conformation dependent library (CDL) restraints added in 499.3 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 78.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.560A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 150 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.782A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.099A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.558A pdb=" N ASN A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 Proline residue: A 310 - end of helix Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.692A pdb=" N SER B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.664A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 149 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 169 through 187 Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.597A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 332 Proline residue: B 310 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1140 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: 1.15 Time building geometry restraints manager: 1.30 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: 645 1.31 - 1.44: 1215 1.44 - 1.56: 2638 1.56 - 1.69: 12 1.69 - 1.81: 50 Bond restraints: 4560 Sorted by residual: bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.324 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C21 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.331 1.383 -0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 4555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 6109 2.82 - 5.63: 64 5.63 - 8.45: 14 8.45 - 11.26: 0 11.26 - 14.08: 2 Bond angle restraints: 6189 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 109.59 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.95 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD2 TRP B 229 " ideal model delta sigma weight residual 126.80 131.57 -4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD1 TRP B 229 " ideal model delta sigma weight residual 126.90 122.30 4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C32 PC1 A 601 " pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 111.44 119.80 -8.36 3.00e+00 1.11e-01 7.76e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2452 17.56 - 35.12: 196 35.12 - 52.68: 42 52.68 - 70.25: 7 70.25 - 87.81: 5 Dihedral angle restraints: 2702 sinusoidal: 1080 harmonic: 1622 Sorted by residual: dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N TRP B 229 " pdb=" CA TRP B 229 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual -180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 560 0.040 - 0.080: 152 0.080 - 0.119: 46 0.119 - 0.159: 3 0.159 - 0.199: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA TRP B 229 " pdb=" N TRP B 229 " pdb=" C TRP B 229 " pdb=" CB TRP B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB ILE B 225 " pdb=" CA ILE B 225 " pdb=" CG1 ILE B 225 " pdb=" CG2 ILE B 225 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 759 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 229 " -0.028 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 229 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 229 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 229 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 229 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " -0.016 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP A 229 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 253 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.035 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 714 2.76 - 3.30: 4279 3.30 - 3.83: 7391 3.83 - 4.37: 8110 4.37 - 4.90: 15202 Nonbonded interactions: 35696 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" NH2 ARG A 144 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 58 " pdb=" OH TYR B 103 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 176 " model vdw 2.320 3.040 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR A 202 " pdb=" OD1 ASP A 205 " model vdw 2.347 3.040 ... (remaining 35691 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 'A' and (resid 44 through 111 or resid 115 through 327 or resid 601)) selection = (chain 'B' and (resid 44 through 151 or (resid 152 and (name N or name CA or nam \ e C or name O or name CB )) or resid 160 or (resid 161 and (name N or name CA or \ name C or name O or name CB )) or resid 162 through 327 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: 5.750 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.080 Find NCS groups from input model: 0.180 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 0.200 4562 Z= 0.349 Angle : 0.798 14.077 6193 Z= 0.379 Chirality : 0.040 0.199 762 Planarity : 0.005 0.062 721 Dihedral : 14.107 87.807 1648 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 555 helix: 2.86 (0.23), residues: 421 sheet: 1.83 (0.89), residues: 38 loop : -2.06 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP B 229 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE A 308 TYR 0.010 0.001 TYR B 103 ARG 0.003 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.12636 ( 381) hydrogen bonds : angle 4.89650 ( 1140) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.26980 ( 4) covalent geometry : bond 0.00717 ( 4560) covalent geometry : angle 0.79852 ( 6189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.513 Fit side-chains REVERT: A 79 ILE cc_start: 0.7930 (mm) cc_final: 0.7647 (mm) REVERT: A 199 MET cc_start: 0.7318 (ttm) cc_final: 0.6938 (ttm) REVERT: A 275 PHE cc_start: 0.8136 (t80) cc_final: 0.7924 (t80) REVERT: B 174 MET cc_start: 0.6158 (mmm) cc_final: 0.5737 (mmm) REVERT: B 193 GLN cc_start: 0.7231 (tt0) cc_final: 0.6882 (tt0) REVERT: B 283 SER cc_start: 0.8344 (m) cc_final: 0.8064 (t) REVERT: B 312 LEU cc_start: 0.7856 (mp) cc_final: 0.7587 (mt) outliers start: 0 outliers final: 1 residues processed: 81 average time/residue: 0.7228 time to fit residues: 62.3310 Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 255 ASN B 256 GLN B 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114345 restraints weight = 5528.114| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.96 r_work: 0.3441 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4562 Z= 0.232 Angle : 0.602 6.592 6193 Z= 0.313 Chirality : 0.044 0.179 762 Planarity : 0.005 0.052 721 Dihedral : 11.429 77.156 686 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 7.85 % Favored : 90.54 % 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: 3.17 (0.34), residues: 555 helix: 2.88 (0.22), residues: 432 sheet: 3.08 (0.98), residues: 27 loop : -2.26 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 229 HIS 0.001 0.001 HIS B 214 PHE 0.023 0.002 PHE B 215 TYR 0.015 0.002 TYR B 280 ARG 0.006 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 381) hydrogen bonds : angle 4.16259 ( 1140) SS BOND : bond 0.00508 ( 2) SS BOND : angle 0.46301 ( 4) covalent geometry : bond 0.00565 ( 4560) covalent geometry : angle 0.60201 ( 6189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.541 Fit side-chains REVERT: A 79 ILE cc_start: 0.8194 (mm) cc_final: 0.7948 (mm) REVERT: A 195 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7889 (pp) REVERT: A 200 THR cc_start: 0.8333 (m) cc_final: 0.7831 (p) REVERT: B 72 ILE cc_start: 0.8625 (mm) cc_final: 0.8421 (mt) REVERT: B 174 MET cc_start: 0.6741 (mmm) cc_final: 0.6307 (mmm) REVERT: B 199 MET cc_start: 0.7529 (mtm) cc_final: 0.7291 (mtm) outliers start: 8 outliers final: 2 residues processed: 74 average time/residue: 0.5719 time to fit residues: 45.7918 Evaluate side-chains 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116677 restraints weight = 5558.206| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.96 r_work: 0.3475 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4562 Z= 0.125 Angle : 0.490 6.220 6193 Z= 0.267 Chirality : 0.038 0.167 762 Planarity : 0.005 0.056 721 Dihedral : 10.754 73.191 686 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.61 % Allowed : 9.46 % Favored : 88.93 % 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: 3.51 (0.34), residues: 555 helix: 3.24 (0.22), residues: 430 sheet: 2.28 (1.48), residues: 12 loop : -1.64 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.002 0.000 HIS A 214 PHE 0.027 0.001 PHE B 215 TYR 0.007 0.001 TYR A 280 ARG 0.004 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 381) hydrogen bonds : angle 3.88110 ( 1140) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.40070 ( 4) covalent geometry : bond 0.00268 ( 4560) covalent geometry : angle 0.48977 ( 6189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.479 Fit side-chains REVERT: A 79 ILE cc_start: 0.8158 (mm) cc_final: 0.7926 (mm) REVERT: A 187 ASP cc_start: 0.7799 (p0) cc_final: 0.7585 (p0) REVERT: A 279 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8126 (tpp-160) REVERT: B 174 MET cc_start: 0.6720 (mmm) cc_final: 0.6279 (mmm) REVERT: B 199 MET cc_start: 0.7569 (mtm) cc_final: 0.7273 (mtm) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.6273 time to fit residues: 47.2065 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 50 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 37 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116565 restraints weight = 5513.061| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.94 r_work: 0.3473 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4562 Z= 0.128 Angle : 0.527 13.820 6193 Z= 0.270 Chirality : 0.039 0.190 762 Planarity : 0.005 0.058 721 Dihedral : 10.443 75.482 684 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.41 % Allowed : 12.27 % Favored : 86.32 % 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: 3.76 (0.34), residues: 555 helix: 3.35 (0.21), residues: 431 sheet: 2.24 (1.49), residues: 12 loop : -1.29 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.001 0.000 HIS A 73 PHE 0.027 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 381) hydrogen bonds : angle 3.79980 ( 1140) SS BOND : bond 0.00339 ( 2) SS BOND : angle 0.46715 ( 4) covalent geometry : bond 0.00279 ( 4560) covalent geometry : angle 0.52739 ( 6189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.473 Fit side-chains REVERT: A 79 ILE cc_start: 0.8135 (mm) cc_final: 0.7898 (mm) REVERT: A 279 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7960 (tpp-160) REVERT: B 174 MET cc_start: 0.6786 (mmm) cc_final: 0.6343 (mmm) REVERT: B 199 MET cc_start: 0.7686 (mtm) cc_final: 0.7201 (mtm) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.7032 time to fit residues: 51.2703 Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114909 restraints weight = 5610.771| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.97 r_work: 0.3446 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4562 Z= 0.182 Angle : 0.553 12.022 6193 Z= 0.289 Chirality : 0.041 0.175 762 Planarity : 0.005 0.058 721 Dihedral : 10.818 78.389 684 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 11.87 % Favored : 85.92 % 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: 3.69 (0.33), residues: 555 helix: 3.24 (0.22), residues: 430 sheet: 2.68 (0.99), residues: 24 loop : -1.60 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.001 0.000 HIS B 282 PHE 0.027 0.002 PHE B 215 TYR 0.012 0.001 TYR B 280 ARG 0.003 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 381) hydrogen bonds : angle 3.86798 ( 1140) SS BOND : bond 0.00382 ( 2) SS BOND : angle 0.54488 ( 4) covalent geometry : bond 0.00433 ( 4560) covalent geometry : angle 0.55290 ( 6189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.490 Fit side-chains REVERT: A 79 ILE cc_start: 0.8157 (mm) cc_final: 0.7926 (mm) REVERT: A 200 THR cc_start: 0.8201 (m) cc_final: 0.7885 (p) REVERT: A 279 ARG cc_start: 0.8531 (tpp80) cc_final: 0.7952 (tpp-160) REVERT: B 174 MET cc_start: 0.6891 (mmm) cc_final: 0.6420 (mmm) REVERT: B 199 MET cc_start: 0.7713 (mtm) cc_final: 0.7216 (mtt) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.6163 time to fit residues: 48.4523 Evaluate side-chains 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 266 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 4 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115547 restraints weight = 5502.650| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.94 r_work: 0.3455 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4562 Z= 0.159 Angle : 0.541 11.447 6193 Z= 0.280 Chirality : 0.040 0.208 762 Planarity : 0.005 0.058 721 Dihedral : 10.793 78.845 684 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.61 % Allowed : 13.08 % Favored : 85.31 % 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: 3.76 (0.34), residues: 555 helix: 3.29 (0.22), residues: 430 sheet: 2.53 (0.99), residues: 24 loop : -1.49 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 315 HIS 0.000 0.000 HIS B 214 PHE 0.029 0.002 PHE B 215 TYR 0.010 0.001 TYR B 280 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 381) hydrogen bonds : angle 3.82950 ( 1140) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.45793 ( 4) covalent geometry : bond 0.00372 ( 4560) covalent geometry : angle 0.54082 ( 6189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.452 Fit side-chains REVERT: A 79 ILE cc_start: 0.8149 (mm) cc_final: 0.7912 (mm) REVERT: A 122 THR cc_start: 0.8201 (t) cc_final: 0.7983 (p) REVERT: A 200 THR cc_start: 0.8189 (m) cc_final: 0.7899 (p) REVERT: A 279 ARG cc_start: 0.8534 (tpp80) cc_final: 0.7950 (tpp-160) REVERT: B 123 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6270 (ptp-170) REVERT: B 149 PHE cc_start: 0.7571 (m-80) cc_final: 0.6472 (t80) REVERT: B 174 MET cc_start: 0.6913 (mmm) cc_final: 0.6445 (mmm) REVERT: B 199 MET cc_start: 0.7745 (mtm) cc_final: 0.7274 (mtt) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.6459 time to fit residues: 49.7166 Evaluate side-chains 71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.135732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114910 restraints weight = 5502.117| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.93 r_work: 0.3445 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4562 Z= 0.191 Angle : 0.562 14.078 6193 Z= 0.291 Chirality : 0.042 0.195 762 Planarity : 0.005 0.057 721 Dihedral : 11.000 81.692 684 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.62 % Allowed : 12.07 % Favored : 85.31 % 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: 3.61 (0.33), residues: 555 helix: 3.19 (0.22), residues: 429 sheet: 2.43 (0.95), residues: 24 loop : -1.55 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.001 0.000 HIS B 248 PHE 0.031 0.002 PHE B 215 TYR 0.012 0.001 TYR B 280 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 381) hydrogen bonds : angle 3.87839 ( 1140) SS BOND : bond 0.00426 ( 2) SS BOND : angle 0.49768 ( 4) covalent geometry : bond 0.00461 ( 4560) covalent geometry : angle 0.56198 ( 6189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.492 Fit side-chains REVERT: A 79 ILE cc_start: 0.8173 (mm) cc_final: 0.7927 (mm) REVERT: A 200 THR cc_start: 0.8175 (m) cc_final: 0.7908 (p) REVERT: B 123 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6340 (ptp-170) REVERT: B 149 PHE cc_start: 0.7577 (m-80) cc_final: 0.6449 (t80) REVERT: B 174 MET cc_start: 0.6980 (mmm) cc_final: 0.6509 (mmm) REVERT: B 199 MET cc_start: 0.7767 (mtm) cc_final: 0.7314 (mtt) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.6413 time to fit residues: 50.1877 Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116153 restraints weight = 5526.954| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3461 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4562 Z= 0.135 Angle : 0.544 13.237 6193 Z= 0.277 Chirality : 0.039 0.193 762 Planarity : 0.005 0.058 721 Dihedral : 10.810 80.359 684 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 13.68 % Favored : 85.11 % 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: 3.88 (0.33), residues: 555 helix: 3.36 (0.22), residues: 430 sheet: 3.17 (0.84), residues: 30 loop : -1.85 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 315 HIS 0.001 0.000 HIS B 73 PHE 0.030 0.001 PHE B 215 TYR 0.009 0.001 TYR A 280 ARG 0.008 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 381) hydrogen bonds : angle 3.80326 ( 1140) SS BOND : bond 0.00338 ( 2) SS BOND : angle 0.39476 ( 4) covalent geometry : bond 0.00300 ( 4560) covalent geometry : angle 0.54406 ( 6189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.542 Fit side-chains REVERT: A 122 THR cc_start: 0.8170 (t) cc_final: 0.7966 (p) REVERT: A 200 THR cc_start: 0.8168 (m) cc_final: 0.7881 (p) REVERT: A 279 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8211 (tpp-160) REVERT: B 123 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6252 (ptp-170) REVERT: B 149 PHE cc_start: 0.7564 (m-80) cc_final: 0.6450 (t80) REVERT: B 174 MET cc_start: 0.6945 (mmm) cc_final: 0.6441 (mmm) REVERT: B 199 MET cc_start: 0.7728 (mtm) cc_final: 0.7292 (mtt) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.7143 time to fit residues: 52.5938 Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116099 restraints weight = 5548.495| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4562 Z= 0.138 Angle : 0.543 13.050 6193 Z= 0.277 Chirality : 0.040 0.230 762 Planarity : 0.005 0.058 721 Dihedral : 10.722 80.581 684 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.41 % Allowed : 13.88 % Favored : 84.71 % 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 (0.33), residues: 555 helix: 3.34 (0.22), residues: 430 sheet: 3.26 (0.84), residues: 30 loop : -1.71 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 315 HIS 0.001 0.000 HIS B 214 PHE 0.030 0.001 PHE B 215 TYR 0.010 0.001 TYR A 280 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 381) hydrogen bonds : angle 3.79343 ( 1140) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.42299 ( 4) covalent geometry : bond 0.00312 ( 4560) covalent geometry : angle 0.54275 ( 6189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.493 Fit side-chains REVERT: A 122 THR cc_start: 0.8172 (t) cc_final: 0.7969 (p) REVERT: A 200 THR cc_start: 0.8166 (m) cc_final: 0.7884 (p) REVERT: A 279 ARG cc_start: 0.8433 (tpp80) cc_final: 0.8206 (tpp-160) REVERT: B 123 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6252 (ptp-170) REVERT: B 149 PHE cc_start: 0.7466 (m-80) cc_final: 0.6389 (t80) REVERT: B 174 MET cc_start: 0.6984 (mmm) cc_final: 0.6490 (mmm) REVERT: B 199 MET cc_start: 0.7732 (mtm) cc_final: 0.7308 (mtt) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.7185 time to fit residues: 55.1106 Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 6 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 47 optimal weight: 0.1980 chunk 53 optimal weight: 0.0020 overall best weight: 0.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117470 restraints weight = 5495.694| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.93 r_work: 0.3483 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4562 Z= 0.114 Angle : 0.503 12.789 6193 Z= 0.262 Chirality : 0.039 0.190 762 Planarity : 0.005 0.058 721 Dihedral : 10.425 78.509 684 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 14.69 % Favored : 84.31 % 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: 4.07 (0.34), residues: 555 helix: 3.44 (0.22), residues: 431 sheet: 3.44 (0.85), residues: 30 loop : -1.62 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.030 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 381) hydrogen bonds : angle 3.70996 ( 1140) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.37061 ( 4) covalent geometry : bond 0.00239 ( 4560) covalent geometry : angle 0.50334 ( 6189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.484 Fit side-chains REVERT: A 200 THR cc_start: 0.8157 (m) cc_final: 0.7878 (p) REVERT: B 149 PHE cc_start: 0.7459 (m-80) cc_final: 0.6390 (t80) REVERT: B 174 MET cc_start: 0.6943 (mmm) cc_final: 0.6436 (mmm) REVERT: B 199 MET cc_start: 0.7719 (mtm) cc_final: 0.7308 (mtt) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.6554 time to fit residues: 51.3051 Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 52 optimal weight: 0.0970 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116376 restraints weight = 5595.317| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.95 r_work: 0.3467 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4562 Z= 0.138 Angle : 0.542 12.699 6193 Z= 0.275 Chirality : 0.040 0.194 762 Planarity : 0.005 0.058 721 Dihedral : 10.467 79.867 684 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.01 % Allowed : 15.29 % Favored : 83.70 % 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: 4.02 (0.33), residues: 555 helix: 3.39 (0.21), residues: 431 sheet: 3.46 (0.85), residues: 30 loop : -1.66 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.030 0.001 PHE B 215 TYR 0.009 0.001 TYR A 280 ARG 0.005 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 381) hydrogen bonds : angle 3.73958 ( 1140) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.44279 ( 4) covalent geometry : bond 0.00313 ( 4560) covalent geometry : angle 0.54203 ( 6189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3587.71 seconds wall clock time: 62 minutes 40.72 seconds (3760.72 seconds total)