Starting phenix.real_space_refine on Tue Feb 11 06:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iep_35389/02_2025/8iep_35389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iep_35389/02_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_35389/02_2025/8iep_35389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iep_35389/02_2025/8iep_35389.map" model { file = "/net/cci-nas-00/data/ceres_data/8iep_35389/02_2025/8iep_35389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iep_35389/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.76, per 1000 atoms: 1.07 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: 1.24 Conformation dependent library (CDL) restraints added in 553.1 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: 0.39 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: 1.36 Time building geometry restraints manager: 1.41 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: 4.890 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: 0.050 Process input model: 16.660 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- 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 : 0.489 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: 0.5984 time to fit residues: 56.8099 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 : 0.531 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.130893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113032 restraints weight = 5740.401| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.73 r_work: 0.3430 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4521 Z= 0.286 Angle : 0.570 7.043 6131 Z= 0.302 Chirality : 0.041 0.194 752 Planarity : 0.006 0.066 712 Dihedral : 11.287 82.429 676 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.65 % Allowed : 7.54 % Favored : 89.82 % 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: 3.54 (0.34), residues: 545 helix: 3.08 (0.22), residues: 427 sheet: 2.20 (0.93), residues: 34 loop : -1.91 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 229 HIS 0.001 0.000 HIS C 214 PHE 0.015 0.002 PHE D 318 TYR 0.012 0.001 TYR D 103 ARG 0.002 0.001 ARG D 144 *********************** 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 82 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.514 Fit side-chains REVERT: C 107 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7425 (mt) REVERT: D 279 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8488 (ttm170) outliers start: 13 outliers final: 3 residues processed: 72 average time/residue: 0.6907 time to fit residues: 53.3584 Evaluate side-chains 67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 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: 0.9980 chunk 52 optimal weight: 0.0980 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 0.0970 chunk 50 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 overall best weight: 0.1578 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.131829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114338 restraints weight = 5810.701| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.74 r_work: 0.3452 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2206 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= 0.145 Angle : 0.478 7.974 6131 Z= 0.255 Chirality : 0.037 0.175 752 Planarity : 0.005 0.068 712 Dihedral : 10.488 79.114 676 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.04 % Allowed : 7.74 % 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: 3.87 (0.34), residues: 545 helix: 3.36 (0.22), residues: 428 sheet: 2.67 (1.40), residues: 14 loop : -1.29 (0.60), residues: 103 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 318 TYR 0.009 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 76 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.565 Fit side-chains REVERT: C 107 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7379 (mt) REVERT: D 279 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8431 (ttm170) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 0.6375 time to fit residues: 47.2101 Evaluate side-chains 70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 127 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: 0.0980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.129475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112216 restraints weight = 5732.057| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.69 r_work: 0.3408 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4521 Z= 0.280 Angle : 0.538 7.617 6131 Z= 0.284 Chirality : 0.041 0.197 752 Planarity : 0.005 0.067 712 Dihedral : 11.001 87.371 676 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.85 % Allowed : 9.37 % Favored : 87.78 % 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: 4.01 (0.34), residues: 545 helix: 3.31 (0.22), residues: 430 sheet: 2.70 (0.93), residues: 34 loop : -1.55 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.015 0.002 PHE D 318 TYR 0.011 0.001 TYR C 280 ARG 0.001 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 81 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.478 Fit side-chains REVERT: C 107 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7446 (mt) REVERT: C 148 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8534 (m) REVERT: C 319 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: D 279 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8517 (ttm170) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.6715 time to fit residues: 51.8358 Evaluate side-chains 70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 195 LEU 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 127 LEU Chi-restraints excluded: chain D residue 192 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: 0.8980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN D 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.129744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112214 restraints weight = 5838.475| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.72 r_work: 0.3406 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4521 Z= 0.279 Angle : 0.533 8.905 6131 Z= 0.281 Chirality : 0.041 0.199 752 Planarity : 0.005 0.066 712 Dihedral : 11.275 89.133 676 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.85 % Allowed : 11.00 % Favored : 86.15 % 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: 3.96 (0.34), residues: 545 helix: 3.29 (0.22), residues: 430 sheet: 2.52 (0.88), residues: 34 loop : -1.54 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.014 0.001 PHE D 318 TYR 0.010 0.001 TYR C 280 ARG 0.002 0.000 ARG D 123 *********************** 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 76 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.494 Fit side-chains REVERT: C 56 PHE cc_start: 0.8142 (m-80) cc_final: 0.7658 (m-80) REVERT: C 107 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7505 (mt) REVERT: C 148 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8545 (m) REVERT: C 319 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: D 279 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8468 (ttt90) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.7110 time to fit residues: 51.5574 Evaluate side-chains 70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 195 LEU 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 127 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.0040 overall best weight: 0.3570 ------------------------------------------------------------------------------- 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 = 0.130226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112964 restraints weight = 5714.348| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.69 r_work: 0.3416 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4521 Z= 0.233 Angle : 0.513 7.188 6131 Z= 0.272 Chirality : 0.040 0.202 752 Planarity : 0.005 0.067 712 Dihedral : 11.285 88.289 676 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.44 % Allowed : 12.02 % 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: 4.06 (0.34), residues: 545 helix: 3.39 (0.22), residues: 428 sheet: 2.40 (0.87), residues: 34 loop : -1.55 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 315 HIS 0.001 0.000 HIS C 214 PHE 0.011 0.001 PHE D 318 TYR 0.010 0.001 TYR C 280 ARG 0.001 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 77 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.545 Fit side-chains REVERT: C 148 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8526 (m) REVERT: C 319 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: D 279 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8324 (ttm170) outliers start: 12 outliers final: 6 residues processed: 70 average time/residue: 0.6916 time to fit residues: 51.6818 Evaluate side-chains 69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 127 LEU 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: 0.5980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112272 restraints weight = 5742.814| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.69 r_work: 0.3409 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4521 Z= 0.261 Angle : 0.544 9.506 6131 Z= 0.282 Chirality : 0.041 0.207 752 Planarity : 0.005 0.068 712 Dihedral : 11.519 89.718 676 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 12.83 % 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: 4.02 (0.34), residues: 545 helix: 3.32 (0.22), residues: 430 sheet: 2.36 (0.87), residues: 34 loop : -1.37 (0.67), 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 0.010 0.001 TYR D 103 ARG 0.002 0.000 ARG D 123 *********************** 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 75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.445 Fit side-chains REVERT: C 148 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8536 (m) REVERT: C 149 PHE cc_start: 0.7271 (t80) cc_final: 0.6931 (t80) REVERT: C 319 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: D 279 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8357 (ttm170) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.6744 time to fit residues: 49.6814 Evaluate side-chains 69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 127 LEU 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: 0.7980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111187 restraints weight = 5698.051| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.67 r_work: 0.3390 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4521 Z= 0.372 Angle : 0.618 10.044 6131 Z= 0.314 Chirality : 0.044 0.215 752 Planarity : 0.006 0.069 712 Dihedral : 11.994 84.478 676 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.24 % Allowed : 13.65 % 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: 3.80 (0.34), residues: 545 helix: 3.17 (0.22), residues: 430 sheet: 2.46 (0.88), residues: 34 loop : -1.58 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 284 HIS 0.001 0.000 HIS C 214 PHE 0.018 0.002 PHE C 275 TYR 0.012 0.001 TYR C 146 ARG 0.002 0.000 ARG D 123 *********************** 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 77 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.389 Fit side-chains REVERT: C 56 PHE cc_start: 0.8136 (m-80) cc_final: 0.7600 (m-80) REVERT: C 148 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8568 (m) REVERT: C 149 PHE cc_start: 0.7347 (t80) cc_final: 0.7034 (t80) REVERT: C 319 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: C 326 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6879 (mmm-85) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.7400 time to fit residues: 55.0860 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 209 THR 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 127 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 192 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 19 optimal weight: 0.0010 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 overall best weight: 0.1386 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.130944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113758 restraints weight = 5764.744| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.69 r_work: 0.3450 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4521 Z= 0.154 Angle : 0.540 11.509 6131 Z= 0.271 Chirality : 0.039 0.203 752 Planarity : 0.005 0.066 712 Dihedral : 11.405 82.322 676 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.83 % Allowed : 14.87 % Favored : 83.30 % 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: 4.17 (0.34), residues: 545 helix: 3.45 (0.22), residues: 428 sheet: 2.53 (0.87), residues: 34 loop : -1.42 (0.65), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.001 0.000 HIS D 282 PHE 0.011 0.001 PHE C 275 TYR 0.009 0.001 TYR C 280 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 75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.510 Fit side-chains REVERT: C 56 PHE cc_start: 0.8115 (m-80) cc_final: 0.7610 (m-80) REVERT: C 149 PHE cc_start: 0.7249 (t80) cc_final: 0.6916 (t80) REVERT: C 326 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6864 (mmm-85) REVERT: D 279 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8347 (ttm170) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.7309 time to fit residues: 55.3953 Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 127 LEU 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 7 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.2254 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.130592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113595 restraints weight = 5697.645| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.67 r_work: 0.3432 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3192 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= 0.179 Angle : 0.520 9.262 6131 Z= 0.267 Chirality : 0.038 0.206 752 Planarity : 0.005 0.066 712 Dihedral : 11.413 80.780 676 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.22 % Allowed : 15.68 % Favored : 83.10 % 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: 4.29 (0.34), residues: 545 helix: 3.51 (0.22), residues: 429 sheet: 2.55 (0.88), residues: 34 loop : -1.27 (0.67), residues: 82 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 0.014 0.001 PHE C 275 TYR 0.011 0.001 TYR C 280 ARG 0.002 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 73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.453 Fit side-chains REVERT: C 56 PHE cc_start: 0.8128 (m-80) cc_final: 0.7618 (m-80) REVERT: C 149 PHE cc_start: 0.7262 (t80) cc_final: 0.6937 (t80) REVERT: C 326 ARG cc_start: 0.7147 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: D 279 ARG cc_start: 0.8732 (ttm170) cc_final: 0.8464 (ttm170) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.6812 time to fit residues: 50.9482 Evaluate side-chains 72 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 282 HIS Chi-restraints excluded: chain D residue 127 LEU 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: 0.6980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 45 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.130395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113315 restraints weight = 5762.881| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.68 r_work: 0.3428 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3224 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= 0.189 Angle : 0.537 9.201 6131 Z= 0.271 Chirality : 0.039 0.205 752 Planarity : 0.005 0.066 712 Dihedral : 11.357 77.614 676 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.43 % Allowed : 16.09 % Favored : 82.48 % 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: 4.22 (0.34), residues: 545 helix: 3.49 (0.22), residues: 429 sheet: 2.36 (0.92), residues: 32 loop : -1.27 (0.66), residues: 84 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 0.013 0.001 PHE C 275 TYR 0.011 0.001 TYR C 280 ARG 0.002 0.000 ARG C 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.35 seconds wall clock time: 62 minutes 58.50 seconds (3778.50 seconds total)