Starting phenix.real_space_refine on Thu Jul 2 00:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bf8_16016/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_2026/8bf8_16016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bf8_16016/07_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-dev-6108/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: {'RNA': 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: 1.25, 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: 0.46 Conformation dependent library (CDL) restraints added in 92.3 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: 0.62 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: 0.95 Time building geometry restraints manager: 0.56 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 1.50e-02 4.44e+03 1.82e+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: 7116 1.20 - 2.40: 153 2.40 - 3.60: 34 3.60 - 4.80: 7 4.80 - 5.99: 2 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=" O4' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 108.20 112.12 -3.92 1.50e+00 4.44e-01 6.83e+00 angle pdb=" C2' G B -78 " pdb=" C1' G B -78 " pdb=" N9 G B -78 " ideal model delta sigma weight residual 112.00 114.91 -2.91 1.50e+00 4.44e-01 3.75e+00 angle pdb=" C THR A 123 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " ideal model delta sigma weight residual 122.46 124.93 -2.47 1.41e+00 5.03e-01 3.07e+00 angle pdb=" C2' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 114.00 116.60 -2.60 1.50e+00 4.44e-01 3.00e+00 ... (remaining 7307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2460 17.34 - 34.68: 162 34.68 - 52.02: 71 52.02 - 69.36: 27 69.36 - 86.70: 6 Dihedral angle restraints: 2726 sinusoidal: 1851 harmonic: 875 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -84.08 -75.92 1 1.50e+01 4.44e-03 3.23e+01 dihedral pdb=" CB LYS A 233 " pdb=" CG LYS A 233 " pdb=" CD LYS A 233 " pdb=" CE LYS A 233 " ideal model delta sinusoidal sigma weight residual 60.00 117.41 -57.41 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" O5' C B -67 " pdb=" C5' C B -67 " pdb=" C4' C B -67 " pdb=" C3' C B -67 " ideal model delta sinusoidal sigma weight residual 55.00 -1.26 56.26 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 2723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 796 0.043 - 0.086: 89 0.086 - 0.129: 26 0.129 - 0.171: 0 0.171 - 0.214: 1 Chirality restraints: 912 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR A 309 " pdb=" N TYR A 309 " pdb=" C TYR A 309 " pdb=" CB TYR A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 275 " pdb=" N ILE A 275 " pdb=" C ILE A 275 " pdb=" CB ILE A 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (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: 0.010 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- 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= 0.140 Angle : 0.474 5.995 7312 Z= 0.248 Chirality : 0.031 0.214 912 Planarity : 0.003 0.022 514 Dihedral : 13.850 86.703 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 0.00284 / 0.14 ( 5007) covalent geometry : angle 0.47404 / 0.25 ( 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 : 0.114 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: 0.5380 time to fit residues: 19.6076 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 : 0.111 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 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 = 0.4274 r_free = 0.4274 target = 0.204623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160370 restraints weight = 5137.214| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.36 r_work: 0.3738 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5007 Z= 0.200 Angle : 0.546 6.502 7312 Z= 0.282 Chirality : 0.035 0.200 912 Planarity : 0.004 0.023 514 Dihedral : 13.463 85.196 1657 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: 0.78 (0.50), residues: 292 helix: 1.96 (0.40), residues: 152 sheet: -2.37 (1.40), residues: 16 loop : -0.92 (0.58), residues: 124 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 0.016 0.002 PHE A 35 TRP 0.006 0.002 TRP A 70 HIS 0.004 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 ( 5007) covalent geometry : angle 0.54582 / 0.28 ( 7312) hydrogen bonds : bond 0.05601 / 3.88 ( 256) hydrogen bonds : angle 4.27203 / 3.13 ( 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 : 0.113 Fit side-chains REVERT: A 147 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.6879 (tm130) REVERT: A 168 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 174 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6436 (mt-10) REVERT: A 214 TYR cc_start: 0.8225 (m-80) cc_final: 0.7894 (m-80) REVERT: A 223 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6167 (mmp-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.5077 time to fit residues: 16.4357 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 : 0.113 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.206840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162940 restraints weight = 5168.037| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.33 r_work: 0.3762 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.150 Angle : 0.503 6.146 7312 Z= 0.261 Chirality : 0.033 0.205 912 Planarity : 0.003 0.021 514 Dihedral : 13.369 84.350 1656 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: 0.77 (0.49), residues: 292 helix: 2.10 (0.40), residues: 152 sheet: -1.50 (1.04), residues: 24 loop : -1.26 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.026 0.002 TYR A 309 PHE 0.004 0.001 PHE A 197 TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 5007) covalent geometry : angle 0.50304 / 0.26 ( 7312) hydrogen bonds : bond 0.05036 / 3.46 ( 256) hydrogen bonds : angle 3.92042 / 2.86 ( 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 168 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 223 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6126 (mmp-170) REVERT: A 309 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7367 (p90) outliers start: 5 outliers final: 0 residues processed: 31 average time/residue: 0.5173 time to fit residues: 16.7698 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.201902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156537 restraints weight = 5140.790| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.39 r_work: 0.3694 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5007 Z= 0.267 Angle : 0.606 7.085 7312 Z= 0.311 Chirality : 0.037 0.193 912 Planarity : 0.004 0.029 514 Dihedral : 13.560 83.051 1656 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.72 % Allowed : 15.35 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.48), residues: 292 helix: 1.66 (0.39), residues: 152 sheet: -1.50 (1.04), residues: 24 loop : -1.37 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.033 0.002 TYR A 309 PHE 0.009 0.002 PHE A 197 TRP 0.006 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 ( 5007) covalent geometry : angle 0.60591 / 0.31 ( 7312) hydrogen bonds : bond 0.06231 / 4.39 ( 256) hydrogen bonds : angle 4.20170 / 3.08 ( 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 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.6714 (tm130) REVERT: A 168 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 223 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6250 (mmp-170) REVERT: A 309 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7608 (p90) outliers start: 8 outliers final: 4 residues processed: 30 average time/residue: 0.5797 time to fit residues: 18.1503 Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU 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 228 THR 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: 0.7980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.206056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161806 restraints weight = 5182.055| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.33 r_work: 0.3752 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.157 Angle : 0.516 6.332 7312 Z= 0.267 Chirality : 0.033 0.208 912 Planarity : 0.003 0.021 514 Dihedral : 13.403 81.391 1656 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.79 % Allowed : 16.28 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.39), residues: 152 sheet: -1.50 (1.04), residues: 24 loop : -1.36 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.029 0.002 TYR A 309 PHE 0.004 0.001 PHE A 197 TRP 0.004 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 5007) covalent geometry : angle 0.51558 / 0.27 ( 7312) hydrogen bonds : bond 0.05117 / 3.54 ( 256) hydrogen bonds : angle 3.85865 / 2.83 ( 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 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.109 Fit side-chains REVERT: A 147 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6774 (tm130) REVERT: A 168 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 223 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6130 (mmp-170) REVERT: A 309 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7366 (p90) outliers start: 6 outliers final: 2 residues processed: 27 average time/residue: 0.5665 time to fit residues: 15.9277 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.210044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166496 restraints weight = 5264.110| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.36 r_work: 0.3781 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5007 Z= 0.114 Angle : 0.483 5.921 7312 Z= 0.250 Chirality : 0.031 0.217 912 Planarity : 0.003 0.021 514 Dihedral : 13.275 81.960 1656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.72 % Allowed : 16.74 % 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: 0.97 (0.50), residues: 292 helix: 2.40 (0.39), residues: 152 sheet: -1.70 (1.01), residues: 24 loop : -1.29 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 160 TYR 0.026 0.001 TYR A 309 PHE 0.005 0.001 PHE A 30 TRP 0.004 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 5007) covalent geometry : angle 0.48321 / 0.25 ( 7312) hydrogen bonds : bond 0.04683 / 3.20 ( 256) hydrogen bonds : angle 3.62206 / 2.65 ( 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 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5718 (mtt90) REVERT: A 147 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (tp-100) REVERT: A 168 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 213 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7962 (mtmm) REVERT: A 223 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6171 (mmp-170) REVERT: A 309 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7227 (p90) outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.5936 time to fit residues: 18.5003 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.208883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165096 restraints weight = 5119.088| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.34 r_work: 0.3786 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.140 Angle : 0.492 6.252 7312 Z= 0.254 Chirality : 0.032 0.202 912 Planarity : 0.003 0.021 514 Dihedral : 13.228 82.387 1656 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % 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: 1.03 (0.50), residues: 292 helix: 2.45 (0.39), residues: 152 sheet: -1.62 (1.02), residues: 24 loop : -1.29 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.027 0.001 TYR A 309 PHE 0.004 0.001 PHE A 303 TRP 0.004 0.001 TRP A 300 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 5007) covalent geometry : angle 0.49238 / 0.25 ( 7312) hydrogen bonds : bond 0.04830 / 3.31 ( 256) hydrogen bonds : angle 3.61026 / 2.64 ( 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 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5699 (mtt90) REVERT: A 147 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.6820 (tm130) REVERT: A 168 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 213 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7931 (mtmm) REVERT: A 223 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6174 (mmp-170) REVERT: A 309 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7326 (p90) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.6653 time to fit residues: 19.3172 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.210187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166379 restraints weight = 5262.603| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.36 r_work: 0.3785 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.124 Angle : 0.479 6.039 7312 Z= 0.247 Chirality : 0.031 0.204 912 Planarity : 0.003 0.021 514 Dihedral : 13.174 83.099 1656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % 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: 1.13 (0.50), residues: 292 helix: 2.56 (0.39), residues: 152 sheet: -1.56 (1.03), residues: 24 loop : -1.28 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.025 0.001 TYR A 309 PHE 0.005 0.001 PHE A 303 TRP 0.004 0.001 TRP A 300 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 5007) covalent geometry : angle 0.47881 / 0.25 ( 7312) hydrogen bonds : bond 0.04672 / 3.19 ( 256) hydrogen bonds : angle 3.51789 / 2.57 ( 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: 7 poor density : 22 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5666 (mtt90) REVERT: A 168 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 213 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7904 (mtmm) REVERT: A 223 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6121 (mmp-170) REVERT: A 309 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7274 (p90) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.5956 time to fit residues: 17.3321 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 110 ARG 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.210071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166355 restraints weight = 5132.122| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.33 r_work: 0.3776 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.130 Angle : 0.484 6.183 7312 Z= 0.250 Chirality : 0.031 0.199 912 Planarity : 0.003 0.020 514 Dihedral : 13.134 83.436 1656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.26 % Allowed : 16.74 % Favored : 80.00 % 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: 1.22 (0.50), residues: 292 helix: 2.56 (0.39), residues: 152 sheet: -0.80 (0.94), residues: 34 loop : -1.34 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.026 0.001 TYR A 309 PHE 0.004 0.001 PHE A 303 TRP 0.004 0.001 TRP A 300 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5007) covalent geometry : angle 0.48400 / 0.25 ( 7312) hydrogen bonds : bond 0.04723 / 3.22 ( 256) hydrogen bonds : angle 3.51072 / 2.57 ( 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: 7 poor density : 25 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5681 (mtt90) REVERT: A 147 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.6790 (tm130) REVERT: A 168 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 213 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7916 (mtmm) REVERT: A 223 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6103 (mmp-170) REVERT: A 309 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7325 (p90) outliers start: 7 outliers final: 3 residues processed: 31 average time/residue: 0.6230 time to fit residues: 20.0934 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.204673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163258 restraints weight = 5223.957| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.41 r_work: 0.3709 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5007 Z= 0.221 Angle : 0.560 6.902 7312 Z= 0.290 Chirality : 0.035 0.188 912 Planarity : 0.004 0.024 514 Dihedral : 13.243 82.526 1656 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % 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: 0.80 (0.49), residues: 292 helix: 2.15 (0.39), residues: 152 sheet: -1.45 (1.05), residues: 24 loop : -1.29 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.032 0.002 TYR A 309 PHE 0.007 0.001 PHE A 197 TRP 0.005 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 ( 5007) covalent geometry : angle 0.55972 / 0.29 ( 7312) hydrogen bonds : bond 0.05625 / 3.93 ( 256) hydrogen bonds : angle 3.82117 / 2.80 ( 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 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.110 Fit side-chains REVERT: A 110 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5759 (mtt180) REVERT: A 147 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.6648 (tm130) REVERT: A 168 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 223 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6250 (mmp-170) REVERT: A 309 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7587 (p90) outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.5933 time to fit residues: 17.8885 Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 34 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 121 GLN A 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.205371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164310 restraints weight = 5174.955| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.33 r_work: 0.3716 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5007 Z= 0.198 Angle : 0.544 6.667 7312 Z= 0.282 Chirality : 0.034 0.194 912 Planarity : 0.004 0.021 514 Dihedral : 13.255 82.172 1656 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.72 % Allowed : 17.21 % 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: 0.75 (0.49), residues: 292 helix: 2.13 (0.39), residues: 152 sheet: -1.40 (1.06), residues: 24 loop : -1.35 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.030 0.002 TYR A 309 PHE 0.006 0.001 PHE A 197 TRP 0.005 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 ( 5007) covalent geometry : angle 0.54403 / 0.28 ( 7312) hydrogen bonds : bond 0.05423 / 3.77 ( 256) hydrogen bonds : angle 3.82913 / 2.81 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.31 seconds wall clock time: 31 minutes 36.92 seconds (1896.92 seconds total)