Starting phenix.real_space_refine on Sat May 10 05:07:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4p_37268/05_2025/8w4p_37268.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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 Mg 30 5.21 5 S 1 5.16 5 C 3130 2.51 5 N 695 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4531 Number of models: 1 Model: "" Number of chains: 6 Chain: "p" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1271 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 16, 'TRANS': 197} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 11, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 269 Chain: "4" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 765 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'TRANS': 152} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 153 Planarities with less than four sites: {'UNK:plan-1': 153} Unresolved non-hydrogen planarities: 153 Chain: "3" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 992 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 6, 'TYR%COO:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 432 Unusual residues: {'A86': 1, 'CLA': 9, 'DD6': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 6, 'CLA:plan-4': 9, 'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 95 Chain: "4" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 516 Unusual residues: {'A86': 3, 'CLA': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-3': 8, 'CLA:plan-4': 10, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 113 Chain: "3" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 555 Unusual residues: {'A86': 2, 'CLA': 11, 'DD6': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 7, 'CLA:plan-4': 10, 'CLA:plan-5': 11, 'CLA:plan-6': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 6.04, per 1000 atoms: 1.33 Number of scatterers: 4531 At special positions: 0 Unit cell: (118.72, 113.42, 73.14, 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 Mg 30 11.99 O 675 8.00 N 695 7.00 C 3130 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 581.2 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'p' and resid 62 through 66 Processing helix chain 'p' and resid 83 through 108 removed outlier: 3.622A pdb=" N LEU p 104 " --> pdb=" O GLN p 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 131 through 139 Processing helix chain 'p' and resid 140 through 165 removed outlier: 3.522A pdb=" N ILE p 144 " --> pdb=" O PRO p 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU p 164 " --> pdb=" O ILE p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 169 through 173 Processing helix chain 'p' and resid 190 through 221 removed outlier: 3.795A pdb=" N PHE p 213 " --> pdb=" O MET p 209 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 234 removed outlier: 3.828A pdb=" N GLN p 229 " --> pdb=" O ASP p 225 " (cutoff:3.500A) Proline residue: p 232 - end of helix Processing helix chain '4' and resid 19 through 24 removed outlier: 3.708A pdb=" N UNK 4 24 " --> pdb=" O UNK 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 53 removed outlier: 3.937A pdb=" N UNK 4 29 " --> pdb=" O UNK 4 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK 4 42 " --> pdb=" O UNK 4 38 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N UNK 4 45 " --> pdb=" O UNK 4 41 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N UNK 4 53 " --> pdb=" O UNK 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 102 removed outlier: 4.145A pdb=" N UNK 4 89 " --> pdb=" O UNK 4 85 " (cutoff:3.500A) Processing helix chain '4' and resid 103 through 105 No H-bonds generated for 'chain '4' and resid 103 through 105' Processing helix chain '4' and resid 124 through 128 removed outlier: 3.634A pdb=" N UNK 4 128 " --> pdb=" O UNK 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 160 removed outlier: 4.273A pdb=" N UNK 4 137 " --> pdb=" O UNK 4 133 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 86 Proline residue: 3 83 - end of helix Processing helix chain '3' and resid 98 through 102 Processing helix chain '3' and resid 106 through 112 removed outlier: 3.703A pdb=" N ASN 3 110 " --> pdb=" O VAL 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 129 Processing helix chain '3' and resid 143 through 178 removed outlier: 3.603A pdb=" N LEU 3 163 " --> pdb=" O ARG 3 159 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN 3 178 " --> pdb=" O GLN 3 174 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 1437 1.37 - 1.55: 3208 1.55 - 1.73: 53 1.73 - 1.91: 1 1.91 - 2.09: 120 Bond restraints: 4819 Sorted by residual: bond pdb=" C30 DD6 p 611 " pdb=" C31 DD6 p 611 " ideal model delta sigma weight residual 1.421 1.258 0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C27 DD6 3 303 " pdb=" C29 DD6 3 303 " ideal model delta sigma weight residual 1.418 1.256 0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C30 DD6 3 303 " pdb=" C31 DD6 3 303 " ideal model delta sigma weight residual 1.421 1.261 0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C27 DD6 p 611 " pdb=" C29 DD6 p 611 " ideal model delta sigma weight residual 1.418 1.258 0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C38 A86 4 202 " pdb=" O4 A86 4 202 " ideal model delta sigma weight residual 1.328 1.465 -0.137 2.00e-02 2.50e+03 4.67e+01 ... (remaining 4814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 7091 6.86 - 13.72: 86 13.72 - 20.58: 8 20.58 - 27.44: 3 27.44 - 34.30: 6 Bond angle restraints: 7194 Sorted by residual: angle pdb=" C14 A86 p 610 " pdb=" C15 A86 p 610 " pdb=" O1 A86 p 610 " ideal model delta sigma weight residual 115.67 81.37 34.30 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C14 A86 3 302 " pdb=" C15 A86 3 302 " pdb=" O1 A86 3 302 " ideal model delta sigma weight residual 115.67 83.97 31.70 3.00e+00 1.11e-01 1.12e+02 angle pdb=" C14 A86 4 201 " pdb=" C15 A86 4 201 " pdb=" O1 A86 4 201 " ideal model delta sigma weight residual 115.67 84.11 31.56 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C14 A86 4 203 " pdb=" C15 A86 4 203 " pdb=" O1 A86 4 203 " ideal model delta sigma weight residual 115.67 86.16 29.51 3.00e+00 1.11e-01 9.68e+01 angle pdb=" C14 A86 4 202 " pdb=" C15 A86 4 202 " pdb=" O1 A86 4 202 " ideal model delta sigma weight residual 115.67 86.50 29.17 3.00e+00 1.11e-01 9.45e+01 ... (remaining 7189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 2083 35.29 - 70.58: 77 70.58 - 105.86: 28 105.86 - 141.15: 25 141.15 - 176.44: 3 Dihedral angle restraints: 2216 sinusoidal: 707 harmonic: 1509 Sorted by residual: dihedral pdb=" C34 A86 4 202 " pdb=" C38 A86 4 202 " pdb=" O4 A86 4 202 " pdb=" C39 A86 4 202 " ideal model delta sinusoidal sigma weight residual -177.27 -0.83 -176.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 4 203 " pdb=" C38 A86 4 203 " pdb=" O4 A86 4 203 " pdb=" C39 A86 4 203 " ideal model delta sinusoidal sigma weight residual -177.27 -9.11 -168.16 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C34 A86 3 302 " pdb=" C38 A86 3 302 " pdb=" O4 A86 3 302 " pdb=" C39 A86 3 302 " ideal model delta sinusoidal sigma weight residual 182.73 19.96 162.77 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 2213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 642 0.236 - 0.472: 6 0.472 - 0.709: 2 0.709 - 0.945: 0 0.945 - 1.181: 1 Chirality restraints: 651 Sorted by residual: chirality pdb=" C15 A86 3 301 " pdb=" C14 A86 3 301 " pdb=" C16 A86 3 301 " pdb=" C20 A86 3 301 " both_signs ideal model delta sigma weight residual True 1.20 2.38 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" C20 A86 p 610 " pdb=" C15 A86 p 610 " pdb=" C19 A86 p 610 " pdb=" C21 A86 p 610 " both_signs ideal model delta sigma weight residual True 1.08 1.73 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C15 DD6 3 303 " pdb=" C14 DD6 3 303 " pdb=" C16 DD6 3 303 " pdb=" O1 DD6 3 303 " both_signs ideal model delta sigma weight residual True 1.69 -2.31 -0.62 2.00e-01 2.50e+01 9.52e+00 ... (remaining 648 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 A86 p 610 " 0.006 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C29 A86 p 610 " -0.058 2.00e-02 2.50e+03 pdb=" C30 A86 p 610 " 0.099 2.00e-02 2.50e+03 pdb=" C31 A86 p 610 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 82 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO 3 83 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO 3 83 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO 3 83 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER p 231 " -0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO p 232 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO p 232 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO p 232 " -0.054 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1071 2.83 - 3.34: 4465 3.34 - 3.86: 7602 3.86 - 4.38: 7317 4.38 - 4.90: 11548 Nonbonded interactions: 32003 Sorted by model distance: nonbonded pdb=" C2B CLA p 604 " pdb=" C37 DD6 p 611 " model vdw 2.306 3.680 nonbonded pdb=" CMB CLA p 604 " pdb=" C37 DD6 p 611 " model vdw 2.353 3.880 nonbonded pdb=" NE2 GLN p 200 " pdb=" OBD CLA p 607 " model vdw 2.366 3.120 nonbonded pdb=" O UNK 4 70 " pdb=" N UNK 4 73 " model vdw 2.403 3.120 nonbonded pdb=" N GLN 3 61 " pdb=" OE1 GLN 3 61 " model vdw 2.420 3.120 ... (remaining 31998 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=0.50 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: 17.340 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.030 Find NCS groups from input model: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.025 0.687 4827 Z= 1.986 Angle : 2.000 34.304 7194 Z= 0.765 Chirality : 0.086 1.181 651 Planarity : 0.009 0.107 1033 Dihedral : 27.982 176.439 1238 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.80 % Allowed : 15.28 % Favored : 83.91 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.40), residues: 373 helix: -0.45 (0.35), residues: 175 sheet: None (None), residues: 0 loop : -4.07 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP p 153 HIS 0.006 0.003 HIS p 95 PHE 0.016 0.002 PHE p 213 TYR 0.008 0.001 TYR 3 80 ARG 0.010 0.001 ARG 3 71 Details of bonding type rmsd hydrogen bonds : bond 0.11652 ( 213) hydrogen bonds : angle 5.79234 ( 612) covalent geometry : bond 0.01123 ( 4819) covalent geometry : angle 2.00017 ( 7194) Misc. bond : bond 0.56088 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.328 Fit side-chains REVERT: p 84 ASP cc_start: 0.8634 (p0) cc_final: 0.8299 (p0) REVERT: 3 172 ASP cc_start: 0.8809 (t0) cc_final: 0.8443 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0887 time to fit residues: 4.4093 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051526 restraints weight = 34598.234| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.76 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 4827 Z= 0.196 Angle : 0.884 12.078 7194 Z= 0.359 Chirality : 0.084 0.901 651 Planarity : 0.005 0.079 1033 Dihedral : 27.944 170.788 975 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.72 % Favored : 89.01 % Rotamer: Outliers : 3.20 % Allowed : 12.00 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.41), residues: 373 helix: 0.80 (0.34), residues: 186 sheet: None (None), residues: 0 loop : -3.93 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP p 153 HIS 0.009 0.004 HIS p 95 PHE 0.011 0.001 PHE p 58 TYR 0.006 0.000 TYR 3 80 ARG 0.004 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 213) hydrogen bonds : angle 4.06920 ( 612) covalent geometry : bond 0.00382 ( 4819) covalent geometry : angle 0.88407 ( 7194) Misc. bond : bond 0.07265 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.369 Fit side-chains REVERT: p 84 ASP cc_start: 0.8816 (p0) cc_final: 0.8479 (p0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.0845 time to fit residues: 4.3128 Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.053229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046333 restraints weight = 36549.165| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.62 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.139 4827 Z= 0.468 Angle : 1.149 15.743 7194 Z= 0.479 Chirality : 0.088 0.871 651 Planarity : 0.007 0.068 1033 Dihedral : 27.358 147.591 975 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.87 % Favored : 86.60 % Rotamer: Outliers : 6.40 % Allowed : 12.00 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.43), residues: 373 helix: 0.75 (0.37), residues: 176 sheet: None (None), residues: 0 loop : -3.45 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP p 153 HIS 0.009 0.004 HIS 3 171 PHE 0.019 0.002 PHE p 216 TYR 0.016 0.002 TYR p 245 ARG 0.004 0.001 ARG 3 170 Details of bonding type rmsd hydrogen bonds : bond 0.06098 ( 213) hydrogen bonds : angle 5.19517 ( 612) covalent geometry : bond 0.00941 ( 4819) covalent geometry : angle 1.14857 ( 7194) Misc. bond : bond 0.05781 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.315 Fit side-chains REVERT: p 84 ASP cc_start: 0.9080 (p0) cc_final: 0.8854 (p0) REVERT: 3 80 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8442 (t80) REVERT: 3 172 ASP cc_start: 0.8846 (t0) cc_final: 0.8448 (t0) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.0738 time to fit residues: 3.3376 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain 3 residue 81 VAL Chi-restraints excluded: chain 3 residue 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 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 = 0.3429 r_free = 0.3429 target = 0.054984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047963 restraints weight = 36082.103| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.95 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4827 Z= 0.163 Angle : 0.818 12.721 7194 Z= 0.331 Chirality : 0.085 0.888 651 Planarity : 0.005 0.074 1033 Dihedral : 26.744 143.098 975 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.65 % Favored : 90.08 % Rotamer: Outliers : 4.00 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.45), residues: 373 helix: 1.55 (0.36), residues: 183 sheet: None (None), residues: 0 loop : -3.02 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 157 PHE 0.021 0.001 PHE p 213 TYR 0.006 0.001 TYR p 245 ARG 0.004 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 213) hydrogen bonds : angle 4.08325 ( 612) covalent geometry : bond 0.00324 ( 4819) covalent geometry : angle 0.81844 ( 7194) Misc. bond : bond 0.01928 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.324 Fit side-chains REVERT: p 84 ASP cc_start: 0.9140 (p0) cc_final: 0.8812 (p0) REVERT: 3 80 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8455 (t80) REVERT: 3 172 ASP cc_start: 0.8743 (t0) cc_final: 0.8289 (t0) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.0883 time to fit residues: 4.2402 Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.0000 overall best weight: 3.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 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 = 0.3397 r_free = 0.3397 target = 0.053790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046817 restraints weight = 37202.503| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.98 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 4827 Z= 0.352 Angle : 0.930 12.823 7194 Z= 0.381 Chirality : 0.089 0.915 651 Planarity : 0.005 0.062 1033 Dihedral : 26.458 139.421 975 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.33 % Favored : 87.40 % Rotamer: Outliers : 4.80 % Allowed : 17.60 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.45), residues: 373 helix: 1.66 (0.37), residues: 178 sheet: None (None), residues: 0 loop : -2.83 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 87 HIS 0.004 0.002 HIS p 95 PHE 0.021 0.002 PHE p 213 TYR 0.008 0.001 TYR p 245 ARG 0.002 0.000 ARG 3 87 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 213) hydrogen bonds : angle 4.29323 ( 612) covalent geometry : bond 0.00704 ( 4819) covalent geometry : angle 0.92983 ( 7194) Misc. bond : bond 0.03505 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.338 Fit side-chains REVERT: p 84 ASP cc_start: 0.9151 (p0) cc_final: 0.8899 (p0) REVERT: 3 80 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8539 (t80) REVERT: 3 172 ASP cc_start: 0.8780 (t0) cc_final: 0.8260 (t0) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.0811 time to fit residues: 3.5148 Evaluate side-chains 27 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 224 THR Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 174 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 = 0.3429 r_free = 0.3429 target = 0.054959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047970 restraints weight = 36003.534| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.96 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4827 Z= 0.144 Angle : 0.782 12.569 7194 Z= 0.316 Chirality : 0.086 0.923 651 Planarity : 0.004 0.063 1033 Dihedral : 26.256 141.388 975 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.65 % Favored : 90.08 % Rotamer: Outliers : 4.00 % Allowed : 18.40 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.46), residues: 373 helix: 2.07 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.70 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 87 HIS 0.002 0.001 HIS p 95 PHE 0.022 0.002 PHE p 213 TYR 0.006 0.001 TYR p 245 ARG 0.002 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 213) hydrogen bonds : angle 3.90620 ( 612) covalent geometry : bond 0.00286 ( 4819) covalent geometry : angle 0.78152 ( 7194) Misc. bond : bond 0.01514 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.323 Fit side-chains REVERT: p 84 ASP cc_start: 0.9107 (p0) cc_final: 0.8780 (p0) REVERT: 3 80 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8414 (t80) REVERT: 3 172 ASP cc_start: 0.8706 (t0) cc_final: 0.8172 (t0) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.0830 time to fit residues: 3.9269 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 230 LEU Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 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 = 0.3378 r_free = 0.3378 target = 0.053029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.046202 restraints weight = 37478.469| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.85 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 4827 Z= 0.407 Angle : 1.004 13.387 7194 Z= 0.411 Chirality : 0.090 0.929 651 Planarity : 0.006 0.063 1033 Dihedral : 26.237 138.425 975 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.33 % Favored : 87.40 % Rotamer: Outliers : 6.40 % Allowed : 18.40 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.45), residues: 373 helix: 1.70 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -2.70 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP p 87 HIS 0.005 0.003 HIS p 204 PHE 0.027 0.002 PHE p 213 TYR 0.011 0.001 TYR p 245 ARG 0.004 0.000 ARG p 89 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 213) hydrogen bonds : angle 4.47185 ( 612) covalent geometry : bond 0.00819 ( 4819) covalent geometry : angle 1.00360 ( 7194) Misc. bond : bond 0.03846 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.305 Fit side-chains REVERT: p 84 ASP cc_start: 0.9197 (p0) cc_final: 0.8953 (p0) REVERT: 3 80 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8643 (t80) REVERT: 3 172 ASP cc_start: 0.8868 (t0) cc_final: 0.8331 (t0) outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.0837 time to fit residues: 3.8245 Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 230 LEU Chi-restraints excluded: chain p residue 246 PHE Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 80 TYR Chi-restraints excluded: chain 3 residue 81 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 218 GLN ** 3 174 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 = 0.3434 r_free = 0.3434 target = 0.055071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.048115 restraints weight = 35381.958| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.97 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4827 Z= 0.135 Angle : 0.763 12.763 7194 Z= 0.306 Chirality : 0.086 0.918 651 Planarity : 0.004 0.063 1033 Dihedral : 25.769 136.080 975 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.46), residues: 373 helix: 2.31 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.48 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 87 HIS 0.003 0.001 HIS p 95 PHE 0.026 0.002 PHE p 213 TYR 0.005 0.000 TYR 3 80 ARG 0.002 0.001 ARG 3 71 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 213) hydrogen bonds : angle 3.62733 ( 612) covalent geometry : bond 0.00269 ( 4819) covalent geometry : angle 0.76313 ( 7194) Misc. bond : bond 0.01901 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.389 Fit side-chains REVERT: p 84 ASP cc_start: 0.9126 (p0) cc_final: 0.8792 (p0) REVERT: 3 80 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8438 (t80) REVERT: 3 172 ASP cc_start: 0.8736 (t0) cc_final: 0.8217 (t0) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 0.0990 time to fit residues: 4.6317 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 230 LEU Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 0.0020 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 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 = 0.3429 r_free = 0.3429 target = 0.054829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047886 restraints weight = 35850.482| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.96 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4827 Z= 0.156 Angle : 0.750 12.596 7194 Z= 0.305 Chirality : 0.086 0.922 651 Planarity : 0.004 0.061 1033 Dihedral : 25.523 134.230 975 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.85 % Favored : 90.88 % Rotamer: Outliers : 2.40 % Allowed : 23.20 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.46), residues: 373 helix: 2.32 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.45 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP p 87 HIS 0.002 0.001 HIS p 95 PHE 0.026 0.001 PHE p 213 TYR 0.003 0.000 TYR 3 80 ARG 0.001 0.000 ARG 3 71 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 213) hydrogen bonds : angle 3.59674 ( 612) covalent geometry : bond 0.00317 ( 4819) covalent geometry : angle 0.75016 ( 7194) Misc. bond : bond 0.01896 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.312 Fit side-chains REVERT: p 84 ASP cc_start: 0.9094 (p0) cc_final: 0.8773 (p0) REVERT: 3 80 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8481 (t80) REVERT: 3 172 ASP cc_start: 0.8735 (t0) cc_final: 0.8168 (t0) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.0786 time to fit residues: 3.4162 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 230 LEU Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 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 = 0.3439 r_free = 0.3439 target = 0.055189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048217 restraints weight = 35448.248| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.99 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4827 Z= 0.130 Angle : 0.725 12.361 7194 Z= 0.292 Chirality : 0.086 0.933 651 Planarity : 0.004 0.061 1033 Dihedral : 25.352 132.205 975 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.12 % Favored : 90.62 % Rotamer: Outliers : 3.20 % Allowed : 21.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.46), residues: 373 helix: 2.57 (0.37), residues: 173 sheet: None (None), residues: 0 loop : -2.31 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP p 87 HIS 0.002 0.001 HIS p 95 PHE 0.028 0.002 PHE p 213 TYR 0.003 0.000 TYR 3 80 ARG 0.001 0.000 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 213) hydrogen bonds : angle 3.53719 ( 612) covalent geometry : bond 0.00259 ( 4819) covalent geometry : angle 0.72534 ( 7194) Misc. bond : bond 0.01208 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.332 Fit side-chains REVERT: p 84 ASP cc_start: 0.9145 (p0) cc_final: 0.8796 (p0) REVERT: 3 80 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8456 (t80) REVERT: 3 172 ASP cc_start: 0.8760 (t0) cc_final: 0.8216 (t0) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0815 time to fit residues: 3.6733 Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU Chi-restraints excluded: chain p residue 230 LEU Chi-restraints excluded: chain 3 residue 80 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 174 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 = 0.3432 r_free = 0.3432 target = 0.054952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.047988 restraints weight = 35810.005| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 5.01 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4827 Z= 0.152 Angle : 0.731 12.471 7194 Z= 0.296 Chirality : 0.087 0.933 651 Planarity : 0.004 0.058 1033 Dihedral : 25.183 129.625 975 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.58 % Favored : 91.15 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.46), residues: 373 helix: 2.58 (0.36), residues: 176 sheet: None (None), residues: 0 loop : -2.38 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 87 HIS 0.002 0.001 HIS p 95 PHE 0.024 0.001 PHE p 213 TYR 0.003 0.000 TYR p 245 ARG 0.001 0.000 ARG 3 71 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 213) hydrogen bonds : angle 3.48324 ( 612) covalent geometry : bond 0.00308 ( 4819) covalent geometry : angle 0.73147 ( 7194) Misc. bond : bond 0.01596 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.86 seconds wall clock time: 38 minutes 7.98 seconds (2287.98 seconds total)