Starting phenix.real_space_refine on Fri Aug 22 15:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4p_37268/08_2025/8w4p_37268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4p_37268/08_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_37268/08_2025/8w4p_37268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4p_37268/08_2025/8w4p_37268.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4p_37268/08_2025/8w4p_37268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4p_37268/08_2025/8w4p_37268.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 6, 'PHE:plan': 11, 'ASP:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 7, 'GLU:plan': 11, 'GLN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 7, 'ASP:plan': 9, 'GLN:plan1': 5, 'TYR:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'TYR%COO: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-3': 6, 'CLA:plan-4': 9, 'CLA:plan-5': 9, 'CLA:plan-2': 2} 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-3': 8, 'CLA:plan-4': 10, 'CLA:plan-5': 10, 'CLA:plan-2': 4} 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: 1.29, per 1000 atoms: 0.28 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: 0.44 Conformation dependent library (CDL) restraints added in 85.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.12 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: 0.61 Time building geometry restraints manager: 0.55 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: 14.280 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- 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 : 9.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG 3 71 TYR 0.008 0.001 TYR 3 80 PHE 0.016 0.002 PHE p 213 TRP 0.005 0.001 TRP p 153 HIS 0.006 0.003 HIS p 95 Details of bonding type rmsd covalent geometry : bond 0.01123 ( 4819) covalent geometry : angle 2.00017 ( 7194) hydrogen bonds : bond 0.11652 ( 213) hydrogen bonds : angle 5.79234 ( 612) 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 : 0.115 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: 0.0332 time to fit residues: 1.7281 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 : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.058146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.051187 restraints weight = 35316.201| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.73 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 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 = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 4827 Z= 0.233 Angle : 0.907 13.661 7194 Z= 0.370 Chirality : 0.083 0.853 651 Planarity : 0.006 0.082 1033 Dihedral : 27.868 169.011 975 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.06 % Favored : 87.67 % Rotamer: Outliers : 2.40 % Allowed : 13.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.41), residues: 373 helix: 0.73 (0.35), residues: 185 sheet: None (None), residues: 0 loop : -4.02 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG p 89 TYR 0.006 0.001 TYR 3 80 PHE 0.008 0.001 PHE p 58 TRP 0.005 0.001 TRP p 153 HIS 0.007 0.003 HIS 3 157 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4819) covalent geometry : angle 0.90715 ( 7194) hydrogen bonds : bond 0.05343 ( 213) hydrogen bonds : angle 4.25598 ( 612) Misc. bond : bond 0.08572 ( 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 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.127 Fit side-chains REVERT: p 84 ASP cc_start: 0.8833 (p0) cc_final: 0.8477 (p0) REVERT: 3 172 ASP cc_start: 0.8427 (t0) cc_final: 0.8225 (t0) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.0335 time to fit residues: 1.6163 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 30 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.055356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048368 restraints weight = 36035.599| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.94 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 4827 Z= 0.303 Angle : 0.933 11.903 7194 Z= 0.384 Chirality : 0.089 0.912 651 Planarity : 0.006 0.068 1033 Dihedral : 27.028 150.026 975 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.40 % Favored : 86.33 % Rotamer: Outliers : 4.80 % Allowed : 12.80 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.44), residues: 373 helix: 1.35 (0.36), residues: 180 sheet: None (None), residues: 0 loop : -3.37 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 3 71 TYR 0.008 0.001 TYR 3 80 PHE 0.015 0.002 PHE p 216 TRP 0.006 0.001 TRP p 153 HIS 0.008 0.003 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 4819) covalent geometry : angle 0.93337 ( 7194) hydrogen bonds : bond 0.05073 ( 213) hydrogen bonds : angle 4.25585 ( 612) Misc. bond : bond 0.02552 ( 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 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.080 Fit side-chains REVERT: p 84 ASP cc_start: 0.9115 (p0) cc_final: 0.8811 (p0) REVERT: 3 80 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8494 (t80) REVERT: 3 172 ASP cc_start: 0.8731 (t0) cc_final: 0.8275 (t0) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.0304 time to fit residues: 1.4713 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3458 r_free = 0.3458 target = 0.056179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049341 restraints weight = 35440.499| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.71 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4827 Z= 0.167 Angle : 0.803 12.210 7194 Z= 0.326 Chirality : 0.086 0.902 651 Planarity : 0.005 0.071 1033 Dihedral : 26.788 142.286 975 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.72 % Favored : 89.01 % Rotamer: Outliers : 3.20 % Allowed : 14.40 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.45), residues: 373 helix: 1.80 (0.36), residues: 182 sheet: None (None), residues: 0 loop : -3.20 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 3 159 TYR 0.006 0.001 TYR p 245 PHE 0.009 0.001 PHE p 213 TRP 0.007 0.001 TRP p 87 HIS 0.004 0.001 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4819) covalent geometry : angle 0.80300 ( 7194) hydrogen bonds : bond 0.04739 ( 213) hydrogen bonds : angle 3.91763 ( 612) Misc. bond : bond 0.01078 ( 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 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.111 Fit side-chains REVERT: p 84 ASP cc_start: 0.8959 (p0) cc_final: 0.8631 (p0) REVERT: 3 80 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8315 (t80) REVERT: 3 172 ASP cc_start: 0.8549 (t0) cc_final: 0.8130 (t0) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.0380 time to fit residues: 1.7817 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 45 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 0.0370 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.056374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049540 restraints weight = 35119.919| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.71 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4827 Z= 0.136 Angle : 0.788 12.252 7194 Z= 0.322 Chirality : 0.087 0.927 651 Planarity : 0.005 0.072 1033 Dihedral : 26.715 140.011 975 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.72 % Favored : 89.01 % Rotamer: Outliers : 4.80 % Allowed : 15.20 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.45), residues: 373 helix: 2.10 (0.36), residues: 171 sheet: None (None), residues: 0 loop : -2.81 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG p 89 TYR 0.004 0.000 TYR p 245 PHE 0.017 0.001 PHE p 216 TRP 0.005 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4819) covalent geometry : angle 0.78775 ( 7194) hydrogen bonds : bond 0.04723 ( 213) hydrogen bonds : angle 3.85439 ( 612) Misc. bond : bond 0.01257 ( 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 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.090 Fit side-chains REVERT: p 84 ASP cc_start: 0.8978 (p0) cc_final: 0.8657 (p0) REVERT: 3 80 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8304 (t80) REVERT: 3 172 ASP cc_start: 0.8529 (t0) cc_final: 0.8142 (t0) outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.0301 time to fit residues: 1.5565 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 : 0.079 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.056426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049578 restraints weight = 35787.812| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.73 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4827 Z= 0.136 Angle : 0.787 12.251 7194 Z= 0.321 Chirality : 0.087 0.927 651 Planarity : 0.005 0.072 1033 Dihedral : 26.727 140.006 975 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.72 % Favored : 89.01 % Rotamer: Outliers : 3.20 % Allowed : 16.80 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.45), residues: 373 helix: 2.10 (0.36), residues: 171 sheet: None (None), residues: 0 loop : -2.81 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG p 89 TYR 0.004 0.000 TYR p 245 PHE 0.016 0.001 PHE p 216 TRP 0.005 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4819) covalent geometry : angle 0.78702 ( 7194) hydrogen bonds : bond 0.04726 ( 213) hydrogen bonds : angle 3.85387 ( 612) Misc. bond : bond 0.01256 ( 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 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.070 Fit side-chains REVERT: p 84 ASP cc_start: 0.8979 (p0) cc_final: 0.8658 (p0) REVERT: 3 80 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8307 (t80) REVERT: 3 172 ASP cc_start: 0.8522 (t0) cc_final: 0.8136 (t0) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0261 time to fit residues: 1.1782 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 : 0.076 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.0070 chunk 42 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.4022 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.054473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047484 restraints weight = 36697.793| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.96 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 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 = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4827 Z= 0.287 Angle : 0.895 12.778 7194 Z= 0.366 Chirality : 0.091 0.953 651 Planarity : 0.005 0.063 1033 Dihedral : 26.343 136.837 975 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.80 % Favored : 87.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.46), residues: 373 helix: 1.88 (0.37), residues: 178 sheet: None (None), residues: 0 loop : -2.82 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG p 89 TYR 0.009 0.001 TYR 3 80 PHE 0.013 0.002 PHE p 216 TRP 0.011 0.002 TRP p 87 HIS 0.006 0.002 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 4819) covalent geometry : angle 0.89531 ( 7194) hydrogen bonds : bond 0.04986 ( 213) hydrogen bonds : angle 4.07873 ( 612) Misc. bond : bond 0.01477 ( 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 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.078 Fit side-chains REVERT: p 84 ASP cc_start: 0.9039 (p0) cc_final: 0.8775 (p0) REVERT: 3 80 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8523 (t80) REVERT: 3 172 ASP cc_start: 0.8651 (t0) cc_final: 0.8160 (t0) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.0257 time to fit residues: 1.2266 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 : 0.111 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.055595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048515 restraints weight = 36352.496| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 5.00 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4827 Z= 0.145 Angle : 0.763 12.459 7194 Z= 0.310 Chirality : 0.087 0.925 651 Planarity : 0.004 0.063 1033 Dihedral : 26.075 137.718 975 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.65 % Favored : 90.08 % Rotamer: Outliers : 4.00 % Allowed : 17.60 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.46), residues: 373 helix: 2.27 (0.36), residues: 179 sheet: None (None), residues: 0 loop : -2.70 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 71 TYR 0.005 0.000 TYR p 245 PHE 0.020 0.001 PHE p 213 TRP 0.009 0.001 TRP p 87 HIS 0.003 0.001 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4819) covalent geometry : angle 0.76306 ( 7194) hydrogen bonds : bond 0.04579 ( 213) hydrogen bonds : angle 3.74276 ( 612) Misc. bond : bond 0.01716 ( 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 : 0.076 Fit side-chains REVERT: p 84 ASP cc_start: 0.9095 (p0) cc_final: 0.8749 (p0) REVERT: 3 80 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8501 (t80) REVERT: 3 172 ASP cc_start: 0.8655 (t0) cc_final: 0.8079 (t0) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.0274 time to fit residues: 1.2768 Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.054549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047592 restraints weight = 36226.702| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.87 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4827 Z= 0.238 Angle : 0.827 12.624 7194 Z= 0.337 Chirality : 0.089 0.948 651 Planarity : 0.005 0.059 1033 Dihedral : 25.756 133.667 975 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.26 % Favored : 88.47 % Rotamer: Outliers : 4.00 % Allowed : 17.60 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.46), residues: 373 helix: 2.29 (0.37), residues: 178 sheet: None (None), residues: 0 loop : -2.57 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 87 TYR 0.007 0.001 TYR p 245 PHE 0.029 0.002 PHE p 213 TRP 0.012 0.002 TRP p 87 HIS 0.007 0.002 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4819) covalent geometry : angle 0.82684 ( 7194) hydrogen bonds : bond 0.04702 ( 213) hydrogen bonds : angle 3.85425 ( 612) Misc. bond : bond 0.02687 ( 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 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.164 Fit side-chains REVERT: p 84 ASP cc_start: 0.9103 (p0) cc_final: 0.8819 (p0) REVERT: 3 80 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8558 (t80) REVERT: 3 172 ASP cc_start: 0.8718 (t0) cc_final: 0.8158 (t0) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.0281 time to fit residues: 1.3339 Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.055797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.048742 restraints weight = 35543.328| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 5.05 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 4827 Z= 0.123 Angle : 0.733 12.461 7194 Z= 0.295 Chirality : 0.085 0.912 651 Planarity : 0.004 0.060 1033 Dihedral : 25.531 133.616 975 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.58 % Favored : 91.15 % Rotamer: Outliers : 4.80 % Allowed : 19.20 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.46), residues: 373 helix: 2.73 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -2.39 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 3 71 TYR 0.002 0.000 TYR 3 80 PHE 0.028 0.002 PHE p 213 TRP 0.012 0.001 TRP p 87 HIS 0.003 0.001 HIS p 95 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4819) covalent geometry : angle 0.73293 ( 7194) hydrogen bonds : bond 0.04225 ( 213) hydrogen bonds : angle 3.51659 ( 612) Misc. bond : bond 0.03291 ( 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 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.117 Fit side-chains REVERT: p 84 ASP cc_start: 0.9159 (p0) cc_final: 0.8776 (p0) REVERT: 3 80 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8491 (t80) REVERT: 3 172 ASP cc_start: 0.8612 (t0) cc_final: 0.7998 (t0) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0289 time to fit residues: 1.4389 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 : 0.109 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.053635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.046653 restraints weight = 37620.338| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.99 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 4827 Z= 0.411 Angle : 0.926 13.408 7194 Z= 0.382 Chirality : 0.088 0.915 651 Planarity : 0.005 0.058 1033 Dihedral : 25.425 132.498 975 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.53 % Favored : 88.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.46), residues: 373 helix: 2.17 (0.37), residues: 178 sheet: None (None), residues: 0 loop : -2.39 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG p 89 TYR 0.008 0.001 TYR p 245 PHE 0.027 0.002 PHE p 213 TRP 0.012 0.002 TRP p 87 HIS 0.009 0.003 HIS 3 171 Details of bonding type rmsd covalent geometry : bond 0.00817 ( 4819) covalent geometry : angle 0.92640 ( 7194) hydrogen bonds : bond 0.04897 ( 213) hydrogen bonds : angle 4.07634 ( 612) Misc. bond : bond 0.02837 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 935.91 seconds wall clock time: 16 minutes 42.35 seconds (1002.35 seconds total)