Starting phenix.real_space_refine on Wed Jul 1 23:41:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9x_63743/07_2026/9m9x_63743.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.027 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 K 3 8.98 5 S 28 5.16 5 C 2786 2.51 5 N 683 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4215 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 1 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2052 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 4, 'TRANS': 251} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'ACD': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'ACD': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.24, per 1000 atoms: 0.29 Number of scatterers: 4215 At special positions: 0 Unit cell: (70.47, 78.57, 89.1, 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) K 3 19.00 S 28 16.00 O 715 8.00 N 683 7.00 C 2786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 140.9 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 14 through 65 removed outlier: 4.371A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 165 removed outlier: 3.531A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 220 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 295 removed outlier: 3.717A pdb=" N ILE A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 65 removed outlier: 4.849A pdb=" N LEU B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 164 removed outlier: 3.830A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 217 Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 295 removed outlier: 3.855A pdb=" N ILE B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 944 1.33 - 1.45: 997 1.45 - 1.58: 2334 1.58 - 1.70: 1 1.70 - 1.82: 40 Bond restraints: 4316 Sorted by residual: bond pdb=" CA ALA B 234 " pdb=" CB ALA B 234 " ideal model delta sigma weight residual 1.530 1.418 0.112 1.57e-02 4.06e+03 5.09e+01 bond pdb=" N LEU B 266 " pdb=" CA LEU B 266 " ideal model delta sigma weight residual 1.459 1.409 0.050 1.17e-02 7.31e+03 1.84e+01 bond pdb=" N ALA B 234 " pdb=" CA ALA B 234 " ideal model delta sigma weight residual 1.459 1.413 0.047 1.18e-02 7.18e+03 1.56e+01 bond pdb=" CA SER A 236 " pdb=" CB SER A 236 " ideal model delta sigma weight residual 1.529 1.461 0.069 1.78e-02 3.16e+03 1.49e+01 bond pdb=" CG LEU B 266 " pdb=" CD1 LEU B 266 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 4311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 4463 2.11 - 4.23: 1226 4.23 - 6.34: 136 6.34 - 8.46: 8 8.46 - 10.57: 2 Bond angle restraints: 5835 Sorted by residual: angle pdb=" C VAL A 133 " pdb=" N GLY A 134 " pdb=" CA GLY A 134 " ideal model delta sigma weight residual 120.00 127.07 -7.07 1.10e+00 8.26e-01 4.13e+01 angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 120.21 -6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " pdb=" CG PHE A 235 " ideal model delta sigma weight residual 113.80 119.89 -6.09 1.00e+00 1.00e+00 3.70e+01 angle pdb=" CA PHE B 240 " pdb=" CB PHE B 240 " pdb=" CG PHE B 240 " ideal model delta sigma weight residual 113.80 119.41 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA PHE A 240 " pdb=" CB PHE A 240 " pdb=" CG PHE A 240 " ideal model delta sigma weight residual 113.80 119.20 -5.40 1.00e+00 1.00e+00 2.92e+01 ... (remaining 5830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2360 17.82 - 35.64: 182 35.64 - 53.45: 31 53.45 - 71.27: 9 71.27 - 89.09: 3 Dihedral angle restraints: 2585 sinusoidal: 1096 harmonic: 1489 Sorted by residual: dihedral pdb=" CA THR B 217 " pdb=" C THR B 217 " pdb=" N PRO B 218 " pdb=" CA PRO B 218 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA SER B 39 " pdb=" C SER B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLU A 46 " pdb=" C GLU A 46 " pdb=" N ARG A 47 " pdb=" CA ARG A 47 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 2582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 570 0.140 - 0.280: 65 0.280 - 0.419: 13 0.419 - 0.559: 3 0.559 - 0.699: 1 Chirality restraints: 652 Sorted by residual: chirality pdb=" CG LEU B 266 " pdb=" CB LEU B 266 " pdb=" CD1 LEU B 266 " pdb=" CD2 LEU B 266 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA ALA B 234 " pdb=" N ALA B 234 " pdb=" C ALA B 234 " pdb=" CB ALA B 234 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA LEU B 266 " pdb=" N LEU B 266 " pdb=" C LEU B 266 " pdb=" CB LEU B 266 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.93e+00 ... (remaining 649 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.148 2.00e-02 2.50e+03 8.41e-02 1.42e+02 pdb=" CG TYR B 130 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 257 " -0.142 2.00e-02 2.50e+03 8.21e-02 1.35e+02 pdb=" CG TYR B 257 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 257 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR B 257 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR B 257 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 257 " 0.062 2.00e-02 2.50e+03 pdb=" CZ TYR B 257 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 257 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 53 " -0.082 2.00e-02 2.50e+03 6.07e-02 9.21e+01 pdb=" CG TRP A 53 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 53 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP A 53 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 53 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 53 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP A 53 " 0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 53 " -0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 53 " 0.076 2.00e-02 2.50e+03 pdb=" CH2 TRP A 53 " -0.017 2.00e-02 2.50e+03 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.04: 2235 3.04 - 3.57: 5749 3.57 - 4.09: 7648 4.09 - 4.62: 11799 4.62 - 5.14: 15729 Nonbonded interactions: 43160 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.516 3.040 nonbonded pdb=" OG SER B 246 " pdb=" O2 ACD B 501 " model vdw 2.532 3.040 nonbonded pdb=" OG SER A 246 " pdb=" O2 ACD A 501 " model vdw 2.543 3.040 nonbonded pdb=" O SER A 209 " pdb=" OG SER A 213 " model vdw 2.552 3.040 nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.558 3.040 ... (remaining 43155 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 14 through 164 or resid 191 through 502)) selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 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 : 0.014 0.122 4316 Z= 0.817 Angle : 1.833 10.570 5835 Z= 1.290 Chirality : 0.107 0.699 652 Planarity : 0.016 0.084 717 Dihedral : 13.612 89.086 1631 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.58 % Favored : 98.02 % Rotamer: Outliers : 0.23 % Allowed : 3.43 % Favored : 96.34 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.33), residues: 505 helix: 0.24 (0.22), residues: 407 sheet: None (None), residues: 0 loop : -1.50 (0.60), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 72 TYR 0.148 0.025 TYR B 130 PHE 0.076 0.017 PHE B 225 TRP 0.106 0.028 TRP B 53 HIS 0.008 0.003 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.01374 / 0.82 ( 4316) covalent geometry : angle 1.83256 / 1.29 ( 5835) hydrogen bonds : bond 0.12141 / 8.04 ( 355) hydrogen bonds : angle 6.88734 / 5.07 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 ASN cc_start: 0.7900 (t0) cc_final: 0.7626 (t0) REVERT: B 70 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 152 ILE cc_start: 0.7118 (mt) cc_final: 0.6917 (tp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.3644 time to fit residues: 45.9326 Evaluate side-chains 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS A 288 ASN B 261 ASN B 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.173304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.160370 restraints weight = 6788.216| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.18 r_work: 0.4116 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4316 Z= 0.207 Angle : 0.650 7.563 5835 Z= 0.355 Chirality : 0.042 0.211 652 Planarity : 0.005 0.036 717 Dihedral : 8.631 55.484 725 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 2.97 % Allowed : 10.53 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.35), residues: 505 helix: 1.62 (0.23), residues: 410 sheet: None (None), residues: 0 loop : -0.47 (0.68), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 163 TYR 0.021 0.002 TYR B 130 PHE 0.025 0.003 PHE B 60 TRP 0.017 0.002 TRP B 53 HIS 0.006 0.002 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 ( 4316) covalent geometry : angle 0.65035 / 0.35 ( 5835) hydrogen bonds : bond 0.05747 / 3.93 ( 355) hydrogen bonds : angle 5.00856 / 3.74 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.7321 (tmm) cc_final: 0.7058 (tmm) REVERT: B 56 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7467 (ttp-110) REVERT: B 70 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 198 MET cc_start: 0.7158 (tmm) cc_final: 0.6949 (tmm) REVERT: B 294 MET cc_start: 0.7425 (tpp) cc_final: 0.7198 (mpp) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 0.4255 time to fit residues: 50.2216 Evaluate side-chains 99 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.172712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159883 restraints weight = 6614.827| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.15 r_work: 0.4107 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4316 Z= 0.191 Angle : 0.623 7.187 5835 Z= 0.336 Chirality : 0.041 0.199 652 Planarity : 0.004 0.028 717 Dihedral : 8.349 57.003 725 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.58 % Favored : 98.22 % Rotamer: Outliers : 4.12 % Allowed : 13.73 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.36), residues: 505 helix: 1.75 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.34 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.015 0.002 TYR A 130 PHE 0.029 0.002 PHE A 60 TRP 0.009 0.001 TRP B 53 HIS 0.009 0.002 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 4316) covalent geometry : angle 0.62307 / 0.34 ( 5835) hydrogen bonds : bond 0.05353 / 3.65 ( 355) hydrogen bonds : angle 4.70770 / 3.54 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8074 (t0) cc_final: 0.7657 (t0) REVERT: B 19 ARG cc_start: 0.6943 (ttm110) cc_final: 0.6710 (ttm110) REVERT: B 56 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7521 (ttp-170) REVERT: B 115 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.6336 (ppp) REVERT: B 198 MET cc_start: 0.7231 (tmm) cc_final: 0.6943 (tmm) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 0.4753 time to fit residues: 54.9459 Evaluate side-chains 110 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.171653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.158386 restraints weight = 6660.553| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.20 r_work: 0.4085 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4316 Z= 0.213 Angle : 0.607 7.640 5835 Z= 0.335 Chirality : 0.042 0.205 652 Planarity : 0.004 0.027 717 Dihedral : 8.471 59.495 725 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.39 % Favored : 98.42 % Rotamer: Outliers : 4.12 % Allowed : 17.16 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.35), residues: 505 helix: 1.59 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.68 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.012 0.002 TYR B 257 PHE 0.061 0.003 PHE A 145 TRP 0.008 0.002 TRP B 53 HIS 0.019 0.002 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 ( 4316) covalent geometry : angle 0.60677 / 0.34 ( 5835) hydrogen bonds : bond 0.05395 / 3.67 ( 355) hydrogen bonds : angle 4.72772 / 3.54 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7914 (pmt) REVERT: B 56 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7560 (ttp-110) REVERT: B 115 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.6689 (ppp) REVERT: B 198 MET cc_start: 0.7327 (tmm) cc_final: 0.6993 (tmm) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.4093 time to fit residues: 48.6980 Evaluate side-chains 109 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 164 GLN B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.176049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.163401 restraints weight = 6599.270| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.17 r_work: 0.4140 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4316 Z= 0.157 Angle : 0.556 7.593 5835 Z= 0.308 Chirality : 0.040 0.205 652 Planarity : 0.003 0.020 717 Dihedral : 8.172 54.173 725 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.58 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 19.45 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.35), residues: 505 helix: 1.86 (0.23), residues: 409 sheet: None (None), residues: 0 loop : -0.49 (0.66), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR B 257 PHE 0.028 0.002 PHE A 145 TRP 0.008 0.001 TRP A 95 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 4316) covalent geometry : angle 0.55575 / 0.31 ( 5835) hydrogen bonds : bond 0.04885 / 3.35 ( 355) hydrogen bonds : angle 4.51711 / 3.36 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: B 198 MET cc_start: 0.7316 (tmm) cc_final: 0.6984 (tmm) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.3993 time to fit residues: 46.2424 Evaluate side-chains 107 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 288 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.175982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.163080 restraints weight = 6614.170| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.19 r_work: 0.4136 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4316 Z= 0.167 Angle : 0.569 7.857 5835 Z= 0.315 Chirality : 0.040 0.191 652 Planarity : 0.003 0.028 717 Dihedral : 8.188 53.616 725 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 3.20 % Allowed : 20.82 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.36), residues: 505 helix: 1.90 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.33 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.021 0.001 TYR A 257 PHE 0.023 0.002 PHE A 60 TRP 0.007 0.001 TRP B 53 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 4316) covalent geometry : angle 0.56875 / 0.31 ( 5835) hydrogen bonds : bond 0.04958 / 3.38 ( 355) hydrogen bonds : angle 4.45926 / 3.34 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7582 (ttp-110) REVERT: B 152 ILE cc_start: 0.7597 (tt) cc_final: 0.7377 (pt) REVERT: B 198 MET cc_start: 0.7239 (tmm) cc_final: 0.6911 (tmm) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.3914 time to fit residues: 42.9754 Evaluate side-chains 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 chunk 43 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.3070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 45 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.179502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.166223 restraints weight = 6712.664| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.26 r_work: 0.4168 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4316 Z= 0.137 Angle : 0.555 8.146 5835 Z= 0.311 Chirality : 0.040 0.200 652 Planarity : 0.003 0.026 717 Dihedral : 8.051 52.484 725 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 2.75 % Allowed : 23.34 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.36), residues: 505 helix: 2.20 (0.24), residues: 409 sheet: None (None), residues: 0 loop : -0.14 (0.69), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.027 0.001 TYR A 257 PHE 0.033 0.002 PHE A 145 TRP 0.009 0.001 TRP A 95 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 4316) covalent geometry : angle 0.55523 / 0.31 ( 5835) hydrogen bonds : bond 0.04518 / 3.10 ( 355) hydrogen bonds : angle 4.25071 / 3.18 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.8102 (pmt) cc_final: 0.7664 (pmt) REVERT: B 152 ILE cc_start: 0.7626 (tt) cc_final: 0.7402 (pt) REVERT: B 163 ARG cc_start: 0.6934 (tpm170) cc_final: 0.6501 (tpm170) REVERT: B 198 MET cc_start: 0.7229 (tmm) cc_final: 0.6879 (tmm) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 0.4614 time to fit residues: 46.7539 Evaluate side-chains 96 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 264 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.176009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.162780 restraints weight = 6560.667| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.23 r_work: 0.4127 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4316 Z= 0.201 Angle : 0.593 7.308 5835 Z= 0.330 Chirality : 0.041 0.190 652 Planarity : 0.004 0.034 717 Dihedral : 8.293 54.272 725 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.38 % Favored : 97.43 % Rotamer: Outliers : 3.43 % Allowed : 22.43 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.36), residues: 505 helix: 1.99 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.37 (0.70), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.018 0.002 TYR A 257 PHE 0.027 0.002 PHE A 60 TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 ( 4316) covalent geometry : angle 0.59259 / 0.33 ( 5835) hydrogen bonds : bond 0.05054 / 3.43 ( 355) hydrogen bonds : angle 4.35511 / 3.27 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.8108 (pmt) cc_final: 0.7712 (pmt) REVERT: B 152 ILE cc_start: 0.7655 (tt) cc_final: 0.7431 (pt) REVERT: B 198 MET cc_start: 0.7268 (tmm) cc_final: 0.6925 (tmm) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 0.4254 time to fit residues: 45.8594 Evaluate side-chains 93 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 294 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.176981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.163507 restraints weight = 6651.970| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.27 r_work: 0.4137 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4316 Z= 0.172 Angle : 0.604 8.708 5835 Z= 0.331 Chirality : 0.042 0.245 652 Planarity : 0.004 0.032 717 Dihedral : 8.219 53.068 725 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.03 % Rotamer: Outliers : 3.66 % Allowed : 23.11 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.36), residues: 505 helix: 2.04 (0.23), residues: 410 sheet: None (None), residues: 0 loop : -0.27 (0.70), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.024 0.001 TYR B 257 PHE 0.045 0.002 PHE B 145 TRP 0.007 0.001 TRP A 53 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 4316) covalent geometry : angle 0.60373 / 0.33 ( 5835) hydrogen bonds : bond 0.04876 / 3.32 ( 355) hydrogen bonds : angle 4.32254 / 3.24 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.8059 (pmt) cc_final: 0.7661 (pmt) REVERT: B 152 ILE cc_start: 0.7577 (tt) cc_final: 0.7364 (pt) REVERT: B 163 ARG cc_start: 0.6954 (tpm170) cc_final: 0.6472 (tpm170) REVERT: B 198 MET cc_start: 0.7304 (tmm) cc_final: 0.6953 (tmm) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.4288 time to fit residues: 45.2630 Evaluate side-chains 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 294 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.176753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.163654 restraints weight = 6482.580| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.15 r_work: 0.4140 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4316 Z= 0.180 Angle : 0.605 8.533 5835 Z= 0.332 Chirality : 0.043 0.263 652 Planarity : 0.004 0.032 717 Dihedral : 8.290 56.909 725 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 2.97 % Allowed : 23.57 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.36), residues: 505 helix: 2.01 (0.23), residues: 410 sheet: None (None), residues: 0 loop : -0.34 (0.70), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.025 0.001 TYR B 257 PHE 0.057 0.003 PHE B 145 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 ( 4316) covalent geometry : angle 0.60489 / 0.33 ( 5835) hydrogen bonds : bond 0.04951 / 3.36 ( 355) hydrogen bonds : angle 4.40237 / 3.30 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 MET cc_start: 0.8040 (pmt) cc_final: 0.7600 (pmt) REVERT: B 152 ILE cc_start: 0.7607 (tt) cc_final: 0.7389 (pt) REVERT: B 163 ARG cc_start: 0.6860 (tpm170) cc_final: 0.6463 (tpm170) REVERT: B 198 MET cc_start: 0.7289 (tmm) cc_final: 0.6954 (tmm) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.4353 time to fit residues: 42.7257 Evaluate side-chains 93 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 294 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.177269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164184 restraints weight = 6434.178| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.16 r_work: 0.4147 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4316 Z= 0.172 Angle : 0.603 8.365 5835 Z= 0.330 Chirality : 0.044 0.276 652 Planarity : 0.004 0.031 717 Dihedral : 8.257 57.194 725 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 2.29 % Allowed : 25.17 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.36), residues: 505 helix: 2.07 (0.24), residues: 410 sheet: None (None), residues: 0 loop : -0.31 (0.69), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.025 0.001 TYR B 257 PHE 0.057 0.003 PHE A 145 TRP 0.007 0.001 TRP A 53 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 4316) covalent geometry : angle 0.60269 / 0.33 ( 5835) hydrogen bonds : bond 0.04880 / 3.33 ( 355) hydrogen bonds : angle 4.36156 / 3.27 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.01 seconds wall clock time: 27 minutes 25.61 seconds (1645.61 seconds total)