Starting phenix.real_space_refine on Tue Aug 4 16:27:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bf8_16016/08_2026/8bf8_16016.map" } resolution = 2.8 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 111 5.49 5 S 1 5.16 5 C 2525 2.51 5 N 871 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2303 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2383 Classifications: {'RNAv2': 111} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 94} Chain breaks: 2 Time building chain proxies: 1.28, per 1000 atoms: 0.27 Number of scatterers: 4686 At special positions: 0 Unit cell: (84.032, 87.36, 84.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 P 111 15.00 O 1178 8.00 N 871 7.00 C 2525 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: 0.38 Conformation dependent library (CDL) restraints added in 96.4 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 566 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 53.6% alpha, 16.2% beta 42 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 14 through 43 removed outlier: 3.645A pdb=" N ILE A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 75 through 94 removed outlier: 3.766A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 272 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.057A pdb=" N LYS A 153 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 172 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 157 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 159 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 161 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS A 166 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 171 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 153 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 872 1.33 - 1.45: 1746 1.45 - 1.57: 2169 1.57 - 1.68: 219 1.68 - 1.80: 1 Bond restraints: 5007 Sorted by residual: bond pdb=" O3' C B -63 " pdb=" P C B -62 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.20e-02 6.94e+03 2.84e+00 bond pdb=" C GLY A 189 " pdb=" O GLY A 189 " ideal model delta sigma weight residual 1.243 1.233 0.010 9.30e-03 1.16e+04 1.15e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.25e-01 bond pdb=" CA ILE A 177 " pdb=" CB ILE A 177 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 8.01e-01 bond pdb=" CB PRO A 178 " pdb=" CG PRO A 178 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.39e-01 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 6746 1.20 - 2.40: 262 2.40 - 3.60: 246 3.60 - 4.80: 42 4.80 - 5.99: 16 Bond angle restraints: 7312 Sorted by residual: angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 angle pdb=" O3' A B -76 " pdb=" C3' A B -76 " pdb=" C2' A B -76 " ideal model delta sigma weight residual 113.80 108.12 5.68 2.00e+00 2.50e-01 8.06e+00 angle pdb=" O3' A B -88 " pdb=" C3' A B -88 " pdb=" C2' A B -88 " ideal model delta sigma weight residual 113.80 108.15 5.65 2.00e+00 2.50e-01 7.98e+00 angle pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" O2' G B 1 " ideal model delta sigma weight residual 109.80 114.93 -5.13 2.00e+00 2.50e-01 6.58e+00 angle pdb=" C3' A B 2 " pdb=" C2' A B 2 " pdb=" O2' A B 2 " ideal model delta sigma weight residual 109.80 114.93 -5.13 2.00e+00 2.50e-01 6.57e+00 ... (remaining 7307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 2212 14.62 - 29.23: 226 29.23 - 43.85: 131 43.85 - 58.46: 111 58.46 - 73.08: 46 Dihedral angle restraints: 2726 sinusoidal: 1851 harmonic: 875 Sorted by residual: dihedral pdb=" C4' A B -76 " pdb=" C3' A B -76 " pdb=" C2' A B -76 " pdb=" C1' A B -76 " ideal model delta sinusoidal sigma weight residual 36.34 -36.73 73.08 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' A B -88 " pdb=" C3' A B -88 " pdb=" C2' A B -88 " pdb=" C1' A B -88 " ideal model delta sinusoidal sigma weight residual 36.35 -36.66 73.01 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' A B 2 " pdb=" C3' A B 2 " pdb=" C2' A B 2 " pdb=" C1' A B 2 " ideal model delta sinusoidal sigma weight residual 36.34 -36.47 72.82 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 2723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 710 0.061 - 0.122: 53 0.122 - 0.182: 3 0.182 - 0.243: 111 0.243 - 0.304: 35 Chirality restraints: 912 Sorted by residual: chirality pdb=" C3' A B -88 " pdb=" C4' A B -88 " pdb=" O3' A B -88 " pdb=" C2' A B -88 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2' G B-111 " pdb=" C3' G B-111 " pdb=" O2' G B-111 " pdb=" C1' G B-111 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 909 not shown) Planarity restraints: 514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B -88 " -0.028 2.00e-02 2.50e+03 1.38e-02 5.27e+00 pdb=" N9 A B -88 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A B -88 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -88 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B -88 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B -88 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -78 " 0.026 2.00e-02 2.50e+03 1.08e-02 3.47e+00 pdb=" N9 G B -78 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B -78 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -78 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -78 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B -78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G B -78 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B -78 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B -78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B -78 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 309 " -0.015 2.00e-02 2.50e+03 1.18e-02 2.76e+00 pdb=" CG TYR A 309 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 309 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 309 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 309 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 309 " -0.000 2.00e-02 2.50e+03 ... (remaining 511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 4367 3.28 - 3.82: 9269 3.82 - 4.36: 10882 4.36 - 4.90: 15807 Nonbonded interactions: 40841 Sorted by model distance: nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 238 " pdb=" O6 G B -33 " model vdw 2.243 3.120 nonbonded pdb=" O2' A B -66 " pdb=" O2 C B -63 " model vdw 2.252 3.040 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.284 3.120 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 267 " model vdw 2.307 3.040 ... (remaining 40836 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.090 Find NCS groups from input model: 0.020 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:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.003 0.043 5007 Z= 0.163 Angle : 0.807 5.995 7312 Z= 0.343 Chirality : 0.100 0.304 912 Planarity : 0.003 0.022 514 Dihedral : 19.478 73.080 2160 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.93 % Allowed : 6.98 % Favored : 92.09 % 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: 0.92 (0.51), residues: 292 helix: 2.03 (0.40), residues: 151 sheet: -1.01 (0.85), residues: 44 loop : -0.84 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.029 0.002 TYR A 309 PHE 0.009 0.001 PHE A 35 TRP 0.005 0.001 TRP A 313 HIS 0.005 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 5007) covalent geometry : angle 0.80663 / 0.34 ( 7312) hydrogen bonds : bond 0.13139 / 9.16 ( 256) hydrogen bonds : angle 6.17931 / 4.56 ( 603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.126 Fit side-chains REVERT: A 168 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 214 TYR cc_start: 0.8208 (m-80) cc_final: 0.7977 (m-80) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.5340 time to fit residues: 19.4016 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 64 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 147 GLN A 156 ASN A 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.206551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162093 restraints weight = 5142.330| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.31 r_work: 0.3750 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5007 Z= 0.235 Angle : 1.100 13.027 7312 Z= 0.461 Chirality : 0.094 0.809 912 Planarity : 0.004 0.021 514 Dihedral : 17.274 142.083 1657 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.86 % Allowed : 13.49 % Favored : 84.65 % 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: 0.90 (0.50), residues: 292 helix: 1.99 (0.40), residues: 152 sheet: -1.17 (1.28), residues: 21 loop : -0.92 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.029 0.002 TYR A 309 PHE 0.011 0.001 PHE A 35 TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 5007) covalent geometry : angle 1.09995 / 0.46 ( 7312) hydrogen bonds : bond 0.05881 / 3.96 ( 256) hydrogen bonds : angle 4.35989 / 3.19 ( 603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.133 Fit side-chains REVERT: A 147 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.6903 (tm130) REVERT: A 168 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 174 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6490 (mt-10) REVERT: A 214 TYR cc_start: 0.8259 (m-80) cc_final: 0.7914 (m-80) REVERT: A 223 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6166 (mmp-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.3938 time to fit residues: 12.7686 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.209044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164174 restraints weight = 5117.171| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.30 r_work: 0.3778 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5007 Z= 0.198 Angle : 0.938 10.547 7312 Z= 0.392 Chirality : 0.075 0.612 912 Planarity : 0.004 0.021 514 Dihedral : 17.410 149.306 1656 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.33 % Allowed : 14.88 % Favored : 82.79 % 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: 0.74 (0.50), residues: 292 helix: 2.03 (0.40), residues: 152 sheet: -1.28 (1.11), residues: 24 loop : -1.25 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.027 0.002 TYR A 309 PHE 0.005 0.001 PHE A 197 TRP 0.005 0.001 TRP A 70 HIS 0.004 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 ( 5007) covalent geometry : angle 0.93779 / 0.39 ( 7312) hydrogen bonds : bond 0.05619 / 3.80 ( 256) hydrogen bonds : angle 3.98199 / 2.91 ( 603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.108 Fit side-chains REVERT: A 17 GLN cc_start: 0.7071 (mt0) cc_final: 0.6866 (tt0) REVERT: A 168 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 223 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6143 (mmp-170) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 0.4220 time to fit residues: 14.1242 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.207637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162027 restraints weight = 5086.729| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.31 r_work: 0.3760 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5007 Z= 0.218 Angle : 0.935 14.345 7312 Z= 0.392 Chirality : 0.072 0.669 912 Planarity : 0.004 0.021 514 Dihedral : 17.174 146.406 1656 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.33 % Allowed : 18.14 % Favored : 79.53 % 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: 0.69 (0.49), residues: 292 helix: 2.00 (0.39), residues: 152 sheet: -1.33 (1.12), residues: 24 loop : -1.29 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.028 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.006 0.001 TRP A 313 HIS 0.004 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 ( 5007) covalent geometry : angle 0.93492 / 0.39 ( 7312) hydrogen bonds : bond 0.06400 / 4.20 ( 256) hydrogen bonds : angle 4.03351 / 2.94 ( 603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.068 Fit side-chains REVERT: A 168 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7578 (mt-10) REVERT: A 223 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6153 (mmp-170) REVERT: A 309 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7425 (p90) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.4796 time to fit residues: 14.4654 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.210870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165826 restraints weight = 5101.332| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.32 r_work: 0.3798 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5007 Z= 0.173 Angle : 0.868 9.341 7312 Z= 0.363 Chirality : 0.068 0.613 912 Planarity : 0.003 0.019 514 Dihedral : 17.279 148.769 1656 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.86 % Allowed : 19.07 % Favored : 79.07 % 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: 0.87 (0.50), residues: 292 helix: 2.22 (0.39), residues: 152 sheet: -1.26 (1.15), residues: 24 loop : -1.32 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 238 TYR 0.025 0.002 TYR A 309 PHE 0.004 0.001 PHE A 197 TRP 0.006 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 5007) covalent geometry : angle 0.86844 / 0.36 ( 7312) hydrogen bonds : bond 0.05423 / 3.66 ( 256) hydrogen bonds : angle 3.85064 / 2.81 ( 603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.080 Fit side-chains REVERT: A 168 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7479 (mt-10) REVERT: A 223 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6131 (mmp-170) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.4985 time to fit residues: 14.4848 Evaluate side-chains 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162471 restraints weight = 5180.839| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.32 r_work: 0.3764 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5007 Z= 0.212 Angle : 0.896 10.830 7312 Z= 0.377 Chirality : 0.070 0.649 912 Planarity : 0.004 0.020 514 Dihedral : 17.281 152.481 1656 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % Favored : 79.07 % 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: 0.73 (0.49), residues: 292 helix: 2.08 (0.39), residues: 152 sheet: -1.31 (1.12), residues: 24 loop : -1.33 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.027 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.006 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 5007) covalent geometry : angle 0.89615 / 0.38 ( 7312) hydrogen bonds : bond 0.05794 / 3.99 ( 256) hydrogen bonds : angle 3.90573 / 2.86 ( 603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.080 Fit side-chains REVERT: A 147 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6866 (tm130) REVERT: A 168 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 223 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6155 (mmp-170) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 0.4625 time to fit residues: 13.4693 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.211419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166365 restraints weight = 5041.329| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.32 r_work: 0.3802 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5007 Z= 0.177 Angle : 0.863 9.349 7312 Z= 0.363 Chirality : 0.068 0.620 912 Planarity : 0.003 0.020 514 Dihedral : 17.222 149.987 1656 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % Favored : 79.07 % 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: 0.85 (0.49), residues: 292 helix: 2.29 (0.39), residues: 152 sheet: -1.19 (1.14), residues: 24 loop : -1.48 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.026 0.001 TYR A 309 PHE 0.004 0.001 PHE A 197 TRP 0.009 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 5007) covalent geometry : angle 0.86293 / 0.36 ( 7312) hydrogen bonds : bond 0.05408 / 3.72 ( 256) hydrogen bonds : angle 3.79059 / 2.77 ( 603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.115 Fit side-chains REVERT: A 110 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5675 (mtt180) REVERT: A 168 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 174 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 213 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7975 (mtmm) REVERT: A 223 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6145 (mmp-170) outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 0.4994 time to fit residues: 14.0329 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.207720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161912 restraints weight = 5169.347| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.33 r_work: 0.3755 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5007 Z= 0.227 Angle : 0.904 10.706 7312 Z= 0.382 Chirality : 0.071 0.660 912 Planarity : 0.004 0.020 514 Dihedral : 17.216 149.682 1656 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.79 % Allowed : 18.60 % Favored : 78.60 % 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: 0.65 (0.49), residues: 292 helix: 2.09 (0.39), residues: 152 sheet: -1.23 (1.09), residues: 24 loop : -1.54 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.029 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.009 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 ( 5007) covalent geometry : angle 0.90368 / 0.38 ( 7312) hydrogen bonds : bond 0.05876 / 4.10 ( 256) hydrogen bonds : angle 3.90914 / 2.86 ( 603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.066 Fit side-chains REVERT: A 110 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5725 (mtt180) REVERT: A 147 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6843 (tm130) REVERT: A 168 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 223 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6176 (mmp-170) REVERT: A 309 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7589 (p90) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.4588 time to fit residues: 13.3421 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.207681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162157 restraints weight = 5049.955| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.31 r_work: 0.3759 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5007 Z= 0.224 Angle : 0.901 10.211 7312 Z= 0.381 Chirality : 0.070 0.651 912 Planarity : 0.004 0.021 514 Dihedral : 17.201 149.162 1656 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.19 % Allowed : 17.21 % Favored : 78.60 % 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: 0.62 (0.49), residues: 292 helix: 2.08 (0.39), residues: 152 sheet: -1.32 (1.07), residues: 24 loop : -1.56 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.030 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.012 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 ( 5007) covalent geometry : angle 0.90133 / 0.38 ( 7312) hydrogen bonds : bond 0.05853 / 4.09 ( 256) hydrogen bonds : angle 3.91491 / 2.87 ( 603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.069 Fit side-chains REVERT: A 110 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5717 (mtt180) REVERT: A 147 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.6708 (tm130) REVERT: A 168 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 223 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6183 (mmp-170) REVERT: A 309 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7613 (p90) outliers start: 9 outliers final: 3 residues processed: 30 average time/residue: 0.4524 time to fit residues: 14.1228 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.207364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161618 restraints weight = 5153.893| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.33 r_work: 0.3751 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5007 Z= 0.228 Angle : 0.906 9.788 7312 Z= 0.383 Chirality : 0.071 0.655 912 Planarity : 0.004 0.021 514 Dihedral : 17.202 148.550 1656 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.72 % Allowed : 17.67 % Favored : 78.60 % 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: 0.59 (0.49), residues: 292 helix: 2.07 (0.39), residues: 152 sheet: -1.35 (1.06), residues: 24 loop : -1.59 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.030 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.014 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 ( 5007) covalent geometry : angle 0.90572 / 0.38 ( 7312) hydrogen bonds : bond 0.05882 / 4.12 ( 256) hydrogen bonds : angle 3.97513 / 2.91 ( 603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.068 Fit side-chains REVERT: A 110 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5859 (mtt180) REVERT: A 147 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.6270 (tm130) REVERT: A 168 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 174 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: A 223 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6185 (mmp-170) REVERT: A 309 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7613 (p90) outliers start: 8 outliers final: 3 residues processed: 29 average time/residue: 0.4286 time to fit residues: 12.9292 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.207943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162480 restraints weight = 5093.251| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.32 r_work: 0.3761 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5007 Z= 0.213 Angle : 0.895 9.561 7312 Z= 0.378 Chirality : 0.070 0.652 912 Planarity : 0.004 0.020 514 Dihedral : 17.195 147.626 1656 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.72 % Allowed : 17.67 % Favored : 78.60 % 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: 0.60 (0.49), residues: 292 helix: 2.11 (0.39), residues: 152 sheet: -1.38 (1.06), residues: 24 loop : -1.63 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.029 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.016 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 5007) covalent geometry : angle 0.89493 / 0.38 ( 7312) hydrogen bonds : bond 0.05793 / 4.06 ( 256) hydrogen bonds : angle 3.94982 / 2.89 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.01 seconds wall clock time: 25 minutes 25.78 seconds (1525.78 seconds total)