Starting phenix.real_space_refine on Sat Apr 4 21:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m9x_63743/04_2026/9m9x_63743.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m9x_63743/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9m9x_63743/04_2026/9m9x_63743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m9x_63743/04_2026/9m9x_63743.map" model { file = "/net/cci-nas-00/data/ceres_data/9m9x_63743/04_2026/9m9x_63743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m9x_63743/04_2026/9m9x_63743.cif" } 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-2.1rc1-6017/lib/python3.9/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, 53 Unusual residues: {' K': 3, 'ACD': 1, 'CLR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 1.09, per 1000 atoms: 0.26 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: 0.33 Conformation dependent library (CDL) restraints added in 147.4 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: 0.10 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: 0.65 Time building geometry restraints manager: 0.40 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: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.800 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 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 covalent geometry : bond 0.01374 ( 4316) covalent geometry : angle 1.83256 ( 5835) hydrogen bonds : bond 0.12141 ( 355) hydrogen bonds : angle 6.88734 ( 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 : 0.145 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: 0.4074 time to fit residues: 51.2105 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 : 0.161 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4376 r_free = 0.4376 target = 0.173853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.161232 restraints weight = 6750.331| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.15 r_work: 0.4126 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4316 Z= 0.209 Angle : 0.645 7.459 5835 Z= 0.354 Chirality : 0.042 0.209 652 Planarity : 0.004 0.035 717 Dihedral : 8.651 56.041 725 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 2.97 % Allowed : 10.76 % Favored : 86.27 % 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: 1.72 (0.35), residues: 505 helix: 1.58 (0.23), residues: 410 sheet: None (None), residues: 0 loop : -0.66 (0.66), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.020 0.002 TYR B 130 PHE 0.024 0.002 PHE B 60 TRP 0.019 0.002 TRP B 53 HIS 0.007 0.002 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 4316) covalent geometry : angle 0.64509 ( 5835) hydrogen bonds : bond 0.05844 ( 355) hydrogen bonds : angle 4.98476 ( 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 116 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.7268 (tmm) cc_final: 0.7012 (tmm) REVERT: B 70 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6633 (mm-30) REVERT: B 198 MET cc_start: 0.7128 (tmm) cc_final: 0.6924 (tmm) REVERT: B 294 MET cc_start: 0.7371 (tpp) cc_final: 0.7122 (mpp) outliers start: 13 outliers final: 5 residues processed: 109 average time/residue: 0.4467 time to fit residues: 50.6225 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 : 0.152 ------------------------------------------------------------------------------- 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: 0.7980 chunk 10 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4387 r_free = 0.4387 target = 0.174858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.162048 restraints weight = 6644.940| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.16 r_work: 0.4137 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4316 Z= 0.162 Angle : 0.596 7.249 5835 Z= 0.320 Chirality : 0.040 0.202 652 Planarity : 0.004 0.031 717 Dihedral : 8.253 55.146 725 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.58 % Favored : 98.22 % Rotamer: Outliers : 3.20 % Allowed : 13.96 % Favored : 82.84 % 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: 2.28 (0.37), residues: 505 helix: 1.88 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.02 (0.75), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.015 0.001 TYR B 216 PHE 0.025 0.002 PHE A 60 TRP 0.011 0.001 TRP B 53 HIS 0.009 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4316) covalent geometry : angle 0.59563 ( 5835) hydrogen bonds : bond 0.05078 ( 355) hydrogen bonds : angle 4.61385 ( 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 108 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8083 (t0) cc_final: 0.7658 (t0) REVERT: A 115 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7808 (pmt) REVERT: A 198 MET cc_start: 0.7253 (tmm) cc_final: 0.7051 (tmm) REVERT: B 19 ARG cc_start: 0.6883 (ttm110) cc_final: 0.6646 (ttm110) REVERT: B 115 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.6403 (ppp) REVERT: B 198 MET cc_start: 0.7166 (tmm) cc_final: 0.6880 (tmm) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 0.4924 time to fit residues: 52.1663 Evaluate side-chains 97 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.175648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.162567 restraints weight = 6676.218| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.20 r_work: 0.4137 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4316 Z= 0.169 Angle : 0.575 7.386 5835 Z= 0.317 Chirality : 0.040 0.190 652 Planarity : 0.004 0.026 717 Dihedral : 8.205 55.540 725 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.39 % Favored : 98.42 % Rotamer: Outliers : 2.52 % Allowed : 18.31 % Favored : 79.18 % 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: 2.14 (0.36), residues: 505 helix: 1.76 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 0.04 (0.75), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.014 0.001 TYR A 130 PHE 0.034 0.002 PHE A 60 TRP 0.009 0.001 TRP B 53 HIS 0.018 0.002 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4316) covalent geometry : angle 0.57499 ( 5835) hydrogen bonds : bond 0.04977 ( 355) hydrogen bonds : angle 4.51365 ( 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 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 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7824 (pmt) REVERT: A 198 MET cc_start: 0.7377 (tmm) cc_final: 0.7168 (tmm) REVERT: B 115 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.6346 (ppp) REVERT: B 120 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7503 (p) REVERT: B 198 MET cc_start: 0.7315 (tmm) cc_final: 0.7000 (tmm) REVERT: B 236 SER cc_start: 0.7439 (t) cc_final: 0.6903 (p) outliers start: 11 outliers final: 4 residues processed: 104 average time/residue: 0.4484 time to fit residues: 48.5543 Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 261 ASN A 288 ASN B 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.176797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.164071 restraints weight = 6556.541| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.19 r_work: 0.4147 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4316 Z= 0.168 Angle : 0.568 8.172 5835 Z= 0.313 Chirality : 0.041 0.195 652 Planarity : 0.003 0.024 717 Dihedral : 8.131 53.700 725 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.58 % Favored : 98.22 % Rotamer: Outliers : 2.97 % Allowed : 19.22 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.23 (0.36), residues: 505 helix: 1.83 (0.24), residues: 410 sheet: None (None), residues: 0 loop : 0.07 (0.73), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.020 0.001 TYR A 257 PHE 0.023 0.002 PHE A 60 TRP 0.008 0.001 TRP A 95 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4316) covalent geometry : angle 0.56795 ( 5835) hydrogen bonds : bond 0.04865 ( 355) hydrogen bonds : angle 4.36883 ( 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 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (pmt) REVERT: A 198 MET cc_start: 0.7481 (tmm) cc_final: 0.7278 (tmm) REVERT: B 115 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.6527 (ppp) REVERT: B 125 ILE cc_start: 0.7120 (mp) cc_final: 0.6891 (tp) REVERT: B 198 MET cc_start: 0.7353 (tmm) cc_final: 0.7014 (tmm) outliers start: 13 outliers final: 7 residues processed: 101 average time/residue: 0.4469 time to fit residues: 46.9152 Evaluate side-chains 99 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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 288 ASN 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: 0.8980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 45 HIS B 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.163622 restraints weight = 6685.895| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.23 r_work: 0.4145 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4316 Z= 0.162 Angle : 0.557 8.022 5835 Z= 0.307 Chirality : 0.040 0.226 652 Planarity : 0.003 0.027 717 Dihedral : 8.160 55.200 725 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 3.66 % Allowed : 19.22 % 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: 2.36 (0.36), residues: 505 helix: 1.92 (0.24), residues: 409 sheet: None (None), residues: 0 loop : 0.14 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.020 0.001 TYR A 257 PHE 0.032 0.002 PHE A 145 TRP 0.007 0.001 TRP B 53 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4316) covalent geometry : angle 0.55717 ( 5835) hydrogen bonds : bond 0.04821 ( 355) hydrogen bonds : angle 4.35243 ( 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 107 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7842 (pmt) REVERT: A 198 MET cc_start: 0.7460 (tmm) cc_final: 0.7151 (tmm) REVERT: B 115 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.6584 (ppp) REVERT: B 163 ARG cc_start: 0.6804 (tpm170) cc_final: 0.6382 (tpm170) REVERT: B 198 MET cc_start: 0.7337 (tmm) cc_final: 0.6992 (tmm) outliers start: 16 outliers final: 7 residues processed: 101 average time/residue: 0.4703 time to fit residues: 49.4202 Evaluate side-chains 97 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 288 ASN B 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.178451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.165227 restraints weight = 6669.184| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.25 r_work: 0.4159 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4316 Z= 0.153 Angle : 0.564 7.200 5835 Z= 0.312 Chirality : 0.041 0.227 652 Planarity : 0.004 0.027 717 Dihedral : 8.225 57.164 725 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 3.43 % Allowed : 21.05 % Favored : 75.51 % 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: 2.44 (0.36), residues: 505 helix: 1.97 (0.24), residues: 410 sheet: None (None), residues: 0 loop : 0.18 (0.75), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.023 0.001 TYR A 257 PHE 0.022 0.002 PHE A 145 TRP 0.007 0.001 TRP A 95 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4316) covalent geometry : angle 0.56362 ( 5835) hydrogen bonds : bond 0.04707 ( 355) hydrogen bonds : angle 4.28511 ( 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 99 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (pmt) REVERT: A 198 MET cc_start: 0.7435 (tmm) cc_final: 0.7141 (tmm) REVERT: B 70 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6551 (mm-30) REVERT: B 115 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.6611 (ppp) REVERT: B 198 MET cc_start: 0.7193 (tmm) cc_final: 0.6856 (tmm) outliers start: 15 outliers final: 6 residues processed: 92 average time/residue: 0.5001 time to fit residues: 47.7730 Evaluate side-chains 92 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 115 MET Chi-restraints excluded: chain A residue 130 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 0.0980 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.180678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.168078 restraints weight = 6489.138| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.15 r_work: 0.4190 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4316 Z= 0.139 Angle : 0.559 8.640 5835 Z= 0.308 Chirality : 0.040 0.228 652 Planarity : 0.003 0.028 717 Dihedral : 8.080 58.796 725 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 2.75 % Allowed : 21.74 % Favored : 75.51 % 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: 2.74 (0.37), residues: 505 helix: 2.18 (0.24), residues: 411 sheet: None (None), residues: 0 loop : 0.26 (0.76), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.020 0.001 TYR B 257 PHE 0.045 0.002 PHE A 145 TRP 0.008 0.001 TRP A 95 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4316) covalent geometry : angle 0.55882 ( 5835) hydrogen bonds : bond 0.04465 ( 355) hydrogen bonds : angle 4.13381 ( 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 97 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7804 (pmt) REVERT: A 198 MET cc_start: 0.7332 (tmm) cc_final: 0.7123 (tmm) REVERT: B 70 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 163 ARG cc_start: 0.6707 (tpm170) cc_final: 0.6276 (tpm170) REVERT: B 198 MET cc_start: 0.7146 (tmm) cc_final: 0.6830 (tmm) REVERT: B 236 SER cc_start: 0.7407 (t) cc_final: 0.6900 (p) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.4966 time to fit residues: 46.9120 Evaluate side-chains 91 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 115 MET 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 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: 1.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 47 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4422 r_free = 0.4422 target = 0.178788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.165961 restraints weight = 6544.198| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.17 r_work: 0.4164 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4316 Z= 0.169 Angle : 0.611 10.588 5835 Z= 0.331 Chirality : 0.043 0.267 652 Planarity : 0.004 0.030 717 Dihedral : 8.245 58.888 725 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 2.06 % Allowed : 21.51 % Favored : 76.43 % 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: 2.50 (0.36), residues: 505 helix: 2.04 (0.24), residues: 411 sheet: None (None), residues: 0 loop : 0.03 (0.72), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.017 0.001 TYR B 257 PHE 0.053 0.002 PHE A 145 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4316) covalent geometry : angle 0.61135 ( 5835) hydrogen bonds : bond 0.04763 ( 355) hydrogen bonds : angle 4.27327 ( 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 92 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7333 (tmm) cc_final: 0.7075 (tmm) REVERT: A 235 PHE cc_start: 0.8546 (m-10) cc_final: 0.8318 (m-10) REVERT: A 261 ASN cc_start: 0.8230 (t0) cc_final: 0.8003 (t0) REVERT: B 70 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6575 (mm-30) REVERT: B 163 ARG cc_start: 0.6716 (tpm170) cc_final: 0.6398 (tpm170) REVERT: B 198 MET cc_start: 0.7242 (tmm) cc_final: 0.6928 (tmm) REVERT: B 236 SER cc_start: 0.7449 (t) cc_final: 0.6948 (p) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.4750 time to fit residues: 44.4096 Evaluate side-chains 88 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 20 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.182857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.170305 restraints weight = 6446.592| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.13 r_work: 0.4220 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4316 Z= 0.134 Angle : 0.563 7.694 5835 Z= 0.306 Chirality : 0.042 0.282 652 Planarity : 0.004 0.027 717 Dihedral : 8.053 58.667 725 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 1.83 % Allowed : 22.65 % Favored : 75.51 % 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: 2.84 (0.36), residues: 505 helix: 2.31 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.03 (0.72), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.016 0.001 TYR B 257 PHE 0.052 0.002 PHE A 145 TRP 0.008 0.001 TRP A 95 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4316) covalent geometry : angle 0.56309 ( 5835) hydrogen bonds : bond 0.04389 ( 355) hydrogen bonds : angle 4.08820 ( 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 86 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7217 (tmm) cc_final: 0.6983 (tmm) REVERT: B 70 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6567 (mm-30) REVERT: B 163 ARG cc_start: 0.6591 (tpm170) cc_final: 0.6165 (tpm170) REVERT: B 198 MET cc_start: 0.7128 (tmm) cc_final: 0.6828 (tmm) REVERT: B 236 SER cc_start: 0.7358 (t) cc_final: 0.6868 (p) outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.5104 time to fit residues: 43.8228 Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4414 r_free = 0.4414 target = 0.177805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.164953 restraints weight = 6393.904| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.12 r_work: 0.4155 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4316 Z= 0.187 Angle : 0.632 8.173 5835 Z= 0.345 Chirality : 0.044 0.265 652 Planarity : 0.004 0.032 717 Dihedral : 8.362 58.850 725 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.03 % Rotamer: Outliers : 1.14 % Allowed : 24.26 % Favored : 74.60 % 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: 2.54 (0.36), residues: 505 helix: 2.12 (0.24), residues: 411 sheet: None (None), residues: 0 loop : -0.22 (0.72), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 87 TYR 0.014 0.001 TYR B 257 PHE 0.056 0.003 PHE A 145 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4316) covalent geometry : angle 0.63214 ( 5835) hydrogen bonds : bond 0.04896 ( 355) hydrogen bonds : angle 4.35603 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1549.11 seconds wall clock time: 27 minutes 5.10 seconds (1625.10 seconds total)