Starting phenix.real_space_refine on Thu Jul 24 04:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4p_37268/07_2025/8w4p_37268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4p_37268/07_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_37268/07_2025/8w4p_37268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4p_37268/07_2025/8w4p_37268.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4p_37268/07_2025/8w4p_37268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4p_37268/07_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-5711/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: 5.59, per 1000 atoms: 1.23 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: 2.07 Conformation dependent library (CDL) restraints added in 590.4 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: 0.35 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: 1.03 Time building geometry restraints manager: 2.12 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: 5.400 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- 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 : 0.293 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: 0.0917 time to fit residues: 4.5343 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 : 0.330 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.058453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051589 restraints weight = 34415.177| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.74 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 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 = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 4827 Z= 0.196 Angle : 0.871 11.853 7194 Z= 0.354 Chirality : 0.085 0.900 651 Planarity : 0.005 0.079 1033 Dihedral : 27.919 170.408 975 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.46 % Favored : 89.28 % 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: -2.03 (0.42), residues: 373 helix: 0.86 (0.34), residues: 185 sheet: None (None), residues: 0 loop : -3.93 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP p 153 HIS 0.008 0.004 HIS p 95 PHE 0.010 0.001 PHE p 58 TYR 0.006 0.000 TYR 3 80 ARG 0.003 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 213) hydrogen bonds : angle 4.05656 ( 612) covalent geometry : bond 0.00378 ( 4819) covalent geometry : angle 0.87088 ( 7194) Misc. bond : bond 0.07148 ( 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 : 0.297 Fit side-chains REVERT: p 84 ASP cc_start: 0.8801 (p0) cc_final: 0.8444 (p0) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.1100 time to fit residues: 5.4623 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 : 0.500 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 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: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.052450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.045622 restraints weight = 37017.952| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.42 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.184 4827 Z= 0.543 Angle : 1.267 16.416 7194 Z= 0.527 Chirality : 0.091 0.893 651 Planarity : 0.008 0.071 1033 Dihedral : 27.518 148.852 975 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.80 % Allowed : 13.40 % Favored : 85.79 % Rotamer: Outliers : 6.40 % Allowed : 13.60 % 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: -2.25 (0.43), residues: 373 helix: 0.36 (0.37), residues: 176 sheet: None (None), residues: 0 loop : -3.48 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP p 153 HIS 0.009 0.004 HIS p 204 PHE 0.022 0.003 PHE p 216 TYR 0.019 0.002 TYR p 245 ARG 0.005 0.001 ARG p 89 Details of bonding type rmsd hydrogen bonds : bond 0.06650 ( 213) hydrogen bonds : angle 5.59742 ( 612) covalent geometry : bond 0.01085 ( 4819) covalent geometry : angle 1.26682 ( 7194) Misc. bond : bond 0.08225 ( 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 : 0.385 Fit side-chains REVERT: p 84 ASP cc_start: 0.9139 (p0) cc_final: 0.8937 (p0) REVERT: 3 80 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8431 (t80) REVERT: 3 172 ASP cc_start: 0.8830 (t0) cc_final: 0.8425 (t0) outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 0.1579 time to fit residues: 7.5301 Evaluate side-chains 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 189 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.053901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047153 restraints weight = 36883.210| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.63 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 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 = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 4827 Z= 0.247 Angle : 0.876 13.090 7194 Z= 0.357 Chirality : 0.085 0.889 651 Planarity : 0.005 0.069 1033 Dihedral : 26.769 144.008 975 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.46 % Favored : 89.28 % 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: -1.23 (0.45), residues: 373 helix: 1.29 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -3.08 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 87 HIS 0.004 0.002 HIS 3 157 PHE 0.017 0.001 PHE p 213 TYR 0.007 0.001 TYR p 245 ARG 0.005 0.001 ARG 3 87 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 213) hydrogen bonds : angle 4.34082 ( 612) covalent geometry : bond 0.00494 ( 4819) covalent geometry : angle 0.87609 ( 7194) Misc. bond : bond 0.03179 ( 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 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 1.197 Fit side-chains REVERT: p 84 ASP cc_start: 0.9176 (p0) cc_final: 0.8866 (p0) REVERT: 3 80 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.8580 (t80) REVERT: 3 172 ASP cc_start: 0.8801 (t0) cc_final: 0.8326 (t0) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.1531 time to fit residues: 6.7181 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.052745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045869 restraints weight = 38018.781| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.86 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 4827 Z= 0.434 Angle : 1.038 13.225 7194 Z= 0.425 Chirality : 0.090 0.915 651 Planarity : 0.006 0.065 1033 Dihedral : 26.605 143.405 975 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.40 % Favored : 86.33 % Rotamer: Outliers : 8.80 % Allowed : 16.80 % 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: -1.31 (0.44), residues: 373 helix: 1.09 (0.36), residues: 177 sheet: None (None), residues: 0 loop : -2.94 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP p 87 HIS 0.005 0.002 HIS p 204 PHE 0.017 0.002 PHE p 213 TYR 0.012 0.001 TYR p 245 ARG 0.003 0.001 ARG p 89 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 213) hydrogen bonds : angle 4.77936 ( 612) covalent geometry : bond 0.00864 ( 4819) covalent geometry : angle 1.03811 ( 7194) Misc. bond : bond 0.05730 ( 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 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.353 Fit side-chains REVERT: p 84 ASP cc_start: 0.9217 (p0) cc_final: 0.8981 (p0) REVERT: p 213 PHE cc_start: 0.9383 (t80) cc_final: 0.9182 (t80) REVERT: 3 80 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8536 (t80) REVERT: 3 172 ASP cc_start: 0.8921 (t0) cc_final: 0.8410 (t0) outliers start: 11 outliers final: 7 residues processed: 29 average time/residue: 0.0858 time to fit residues: 4.1958 Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 220 LEU Chi-restraints excluded: chain p residue 224 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.054287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.047611 restraints weight = 36377.058| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.63 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 4827 Z= 0.173 Angle : 0.800 12.861 7194 Z= 0.323 Chirality : 0.085 0.903 651 Planarity : 0.004 0.064 1033 Dihedral : 26.074 141.677 975 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.31 % Favored : 91.42 % Rotamer: Outliers : 3.20 % Allowed : 23.20 % 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: -0.48 (0.45), residues: 373 helix: 1.90 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.67 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP p 87 HIS 0.003 0.001 HIS p 95 PHE 0.021 0.001 PHE p 213 TYR 0.003 0.001 TYR p 245 ARG 0.004 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 213) hydrogen bonds : angle 3.97071 ( 612) covalent geometry : bond 0.00346 ( 4819) covalent geometry : angle 0.80008 ( 7194) Misc. bond : bond 0.03064 ( 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 27 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.352 Fit side-chains REVERT: p 84 ASP cc_start: 0.9172 (p0) cc_final: 0.8848 (p0) REVERT: 3 80 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8470 (t80) REVERT: 3 172 ASP cc_start: 0.8778 (t0) cc_final: 0.8207 (t0) outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.0754 time to fit residues: 3.0092 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 : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 LEU 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: 10.0000 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.052326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.045588 restraints weight = 37712.207| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.82 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.148 4827 Z= 0.469 Angle : 1.038 13.272 7194 Z= 0.423 Chirality : 0.089 0.901 651 Planarity : 0.006 0.063 1033 Dihedral : 26.164 139.480 975 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.26 % Favored : 88.47 % Rotamer: Outliers : 5.60 % Allowed : 22.40 % Favored : 72.00 % 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: -0.86 (0.45), residues: 373 helix: 1.45 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.71 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP p 87 HIS 0.005 0.003 HIS p 95 PHE 0.025 0.002 PHE p 213 TYR 0.009 0.001 TYR p 245 ARG 0.003 0.001 ARG p 89 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 213) hydrogen bonds : angle 4.60406 ( 612) covalent geometry : bond 0.00938 ( 4819) covalent geometry : angle 1.03777 ( 7194) Misc. bond : bond 0.05276 ( 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 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.340 Fit side-chains REVERT: p 84 ASP cc_start: 0.9235 (p0) cc_final: 0.9001 (p0) REVERT: 3 80 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8609 (t80) REVERT: 3 172 ASP cc_start: 0.8911 (t0) cc_final: 0.8400 (t0) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.0844 time to fit residues: 3.7154 Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.053642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046834 restraints weight = 36258.069| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.90 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4827 Z= 0.178 Angle : 0.815 12.713 7194 Z= 0.329 Chirality : 0.086 0.927 651 Planarity : 0.005 0.065 1033 Dihedral : 25.918 141.968 975 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 2.40 % Allowed : 25.60 % Favored : 72.00 % 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: -0.43 (0.46), residues: 373 helix: 1.85 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.54 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 157 PHE 0.026 0.001 PHE p 213 TYR 0.005 0.001 TYR p 245 ARG 0.002 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 213) hydrogen bonds : angle 4.08549 ( 612) covalent geometry : bond 0.00354 ( 4819) covalent geometry : angle 0.81470 ( 7194) Misc. bond : bond 0.03620 ( 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 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.319 Fit side-chains REVERT: p 84 ASP cc_start: 0.9204 (p0) cc_final: 0.8937 (p0) REVERT: 3 80 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8548 (t80) REVERT: 3 172 ASP cc_start: 0.8798 (t0) cc_final: 0.8235 (t0) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0783 time to fit residues: 3.0558 Evaluate side-chains 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 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: 2.9990 chunk 0 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 0.0020 chunk 1 optimal weight: 0.0170 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.4028 ------------------------------------------------------------------------------- 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 = 0.053629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046805 restraints weight = 37082.257| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.84 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4827 Z= 0.178 Angle : 0.815 12.713 7194 Z= 0.329 Chirality : 0.086 0.927 651 Planarity : 0.005 0.065 1033 Dihedral : 25.918 141.968 975 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.04 % Favored : 91.69 % Rotamer: Outliers : 2.40 % Allowed : 24.80 % Favored : 72.80 % 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: -0.43 (0.46), residues: 373 helix: 1.85 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -2.54 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 157 PHE 0.026 0.001 PHE p 213 TYR 0.005 0.001 TYR p 245 ARG 0.002 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 213) hydrogen bonds : angle 4.08549 ( 612) covalent geometry : bond 0.00354 ( 4819) covalent geometry : angle 0.81470 ( 7194) Misc. bond : bond 0.03620 ( 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 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.344 Fit side-chains REVERT: p 84 ASP cc_start: 0.9203 (p0) cc_final: 0.8938 (p0) REVERT: 3 80 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8529 (t80) REVERT: 3 172 ASP cc_start: 0.8789 (t0) cc_final: 0.8220 (t0) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0808 time to fit residues: 3.1704 Evaluate side-chains 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 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: 1.9990 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.053812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047023 restraints weight = 36630.902| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.78 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 4827 Z= 0.168 Angle : 0.804 12.836 7194 Z= 0.325 Chirality : 0.087 0.940 651 Planarity : 0.004 0.063 1033 Dihedral : 25.844 139.645 975 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.19 % Favored : 89.54 % Rotamer: Outliers : 2.40 % Allowed : 25.60 % Favored : 72.00 % 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: -0.29 (0.46), residues: 373 helix: 2.15 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -2.52 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 157 PHE 0.028 0.002 PHE p 213 TYR 0.004 0.000 TYR p 245 ARG 0.002 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 213) hydrogen bonds : angle 3.95390 ( 612) covalent geometry : bond 0.00341 ( 4819) covalent geometry : angle 0.80444 ( 7194) Misc. bond : bond 0.03507 ( 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 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.350 Fit side-chains REVERT: p 84 ASP cc_start: 0.9201 (p0) cc_final: 0.8908 (p0) REVERT: 3 80 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8488 (t80) REVERT: 3 172 ASP cc_start: 0.8780 (t0) cc_final: 0.8218 (t0) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.0837 time to fit residues: 3.4119 Evaluate side-chains 25 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 210 ILE Chi-restraints excluded: chain p residue 215 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: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.053802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.046986 restraints weight = 36484.576| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.84 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 4827 Z= 0.168 Angle : 0.804 12.836 7194 Z= 0.325 Chirality : 0.087 0.940 651 Planarity : 0.004 0.063 1033 Dihedral : 25.844 139.645 975 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.19 % Favored : 89.54 % Rotamer: Outliers : 2.40 % Allowed : 27.20 % Favored : 70.40 % 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: -0.29 (0.46), residues: 373 helix: 2.15 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -2.52 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 157 PHE 0.028 0.002 PHE p 213 TYR 0.004 0.000 TYR p 245 ARG 0.002 0.001 ARG 3 159 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 213) hydrogen bonds : angle 3.95390 ( 612) covalent geometry : bond 0.00341 ( 4819) covalent geometry : angle 0.80444 ( 7194) Misc. bond : bond 0.03507 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.10 seconds wall clock time: 40 minutes 16.14 seconds (2416.14 seconds total)