Starting phenix.real_space_refine on Sun Apr 27 00:55:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.map" model { file = "/net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edc_47944/04_2025/9edc_47944.cif" } resolution = 4.18 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= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 12 5.16 5 C 2596 2.51 5 N 690 2.21 5 O 758 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-5669/modules/chem_data/mon_lib" Total number of atoms: 4062 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2777 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2761 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 338, 2762 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 2816 Chain: "B" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 1.08 Number of scatterers: 4062 At special positions: 0 Unit cell: (73.632, 79.296, 85.904, 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 12 16.00 P 6 15.00 O 758 8.00 N 690 7.00 C 2596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 769.9 milliseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 42.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.835A pdb=" N TYR A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 184 through 188 removed outlier: 4.643A pdb=" N PHE A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.020A pdb=" N TRP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.521A pdb=" N AGLY A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.207A pdb=" N ILE A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.290A pdb=" N THR A 299 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.463A pdb=" N HIS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.500A pdb=" N ILE B 204 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 51 removed outlier: 5.588A pdb=" N ARG A 45 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 61 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 47 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 57 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 121 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 106 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.661A pdb=" N LYS B 220 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.667A pdb=" N VAL B 213 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 184 " --> pdb=" O TRP B 188 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 471 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: 1.01 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 723 1.33 - 1.45: 1093 1.45 - 1.57: 2306 1.57 - 1.69: 16 1.69 - 1.81: 22 Bond restraints: 4160 Sorted by residual: bond pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" O3P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O2P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C PRO B 84 " pdb=" N PRO B 85 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.27e+00 bond pdb=" O1P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 5528 2.71 - 5.43: 87 5.43 - 8.14: 14 8.14 - 10.85: 2 10.85 - 13.57: 2 Bond angle restraints: 5633 Sorted by residual: angle pdb=" C PRO B 85 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " ideal model delta sigma weight residual 121.80 133.13 -11.33 2.44e+00 1.68e-01 2.16e+01 angle pdb=" C THR A 32 " pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta sigma weight residual 110.17 115.24 -5.07 1.11e+00 8.12e-01 2.09e+01 angle pdb=" CB TPO A 197 " pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 119.31 105.74 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N GLN A 96 " pdb=" CA GLN A 96 " pdb=" CB GLN A 96 " ideal model delta sigma weight residual 110.41 117.70 -7.29 1.68e+00 3.54e-01 1.88e+01 angle pdb=" C LEU A 95 " pdb=" N GLN A 96 " pdb=" CA GLN A 96 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 ... (remaining 5628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2264 17.88 - 35.76: 188 35.76 - 53.64: 29 53.64 - 71.52: 8 71.52 - 89.40: 4 Dihedral angle restraints: 2493 sinusoidal: 1038 harmonic: 1455 Sorted by residual: dihedral pdb=" CA LYS B 90 " pdb=" C LYS B 90 " pdb=" N GLY B 91 " pdb=" CA GLY B 91 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA THR A 195 " pdb=" C THR A 195 " pdb=" N TRP A 196 " pdb=" CA TRP A 196 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 201 " pdb=" C THR A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 444 0.052 - 0.104: 118 0.104 - 0.156: 33 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 599 Sorted by residual: chirality pdb=" CB THR A 32 " pdb=" CA THR A 32 " pdb=" OG1 THR A 32 " pdb=" CG2 THR A 32 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR A 32 " pdb=" N THR A 32 " pdb=" C THR A 32 " pdb=" CB THR A 32 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 596 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 32 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 33 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 168 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 169 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 119 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C VAL A 119 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 119 " 0.010 2.00e-02 2.50e+03 pdb=" N MET A 120 " 0.009 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 959 2.79 - 3.32: 3520 3.32 - 3.85: 7147 3.85 - 4.37: 8165 4.37 - 4.90: 13864 Nonbonded interactions: 33655 Sorted by model distance: nonbonded pdb=" OH TYR A 229 " pdb=" O ARG A 256 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" O VAL A 310 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 195 " pdb=" O2P TPO A 197 " model vdw 2.340 3.040 nonbonded pdb=" O PHE A 43 " pdb=" NH1 ARG A 45 " model vdw 2.409 3.120 nonbonded pdb=" NZ LYS A 111 " pdb=" O PHE A 347 " model vdw 2.410 3.120 ... (remaining 33650 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.380 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 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 : 0.005 0.110 4160 Z= 0.245 Angle : 0.883 13.568 5633 Z= 0.482 Chirality : 0.051 0.260 599 Planarity : 0.006 0.065 718 Dihedral : 13.866 89.398 1559 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.43 (0.34), residues: 490 helix: -1.05 (0.33), residues: 192 sheet: -0.34 (0.59), residues: 66 loop : -0.91 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 30 HIS 0.005 0.001 HIS A 142 PHE 0.020 0.002 PHE A 145 TYR 0.019 0.002 TYR B 229 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.16350 ( 169) hydrogen bonds : angle 6.50241 ( 471) covalent geometry : bond 0.00497 ( 4160) covalent geometry : angle 0.88266 ( 5633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6897 (mt) cc_final: 0.6545 (mt) REVERT: A 102 PHE cc_start: 0.9345 (m-80) cc_final: 0.8887 (m-80) REVERT: A 155 GLU cc_start: 0.9257 (tt0) cc_final: 0.8988 (tt0) REVERT: A 179 TYR cc_start: 0.1788 (m-80) cc_final: 0.1450 (m-80) REVERT: A 182 VAL cc_start: 0.9223 (t) cc_final: 0.8916 (p) REVERT: A 221 TRP cc_start: 0.9055 (m100) cc_final: 0.8368 (m100) REVERT: A 222 TRP cc_start: 0.9095 (t-100) cc_final: 0.8763 (t-100) REVERT: A 231 MET cc_start: 0.9110 (mtm) cc_final: 0.8721 (mmm) REVERT: A 236 PRO cc_start: 0.8786 (Cg_endo) cc_final: 0.7453 (Cg_exo) REVERT: A 301 ASP cc_start: 0.7956 (t0) cc_final: 0.7566 (p0) REVERT: A 308 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7859 (mtt90) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3181 time to fit residues: 56.6579 Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.151459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.096065 restraints weight = 17413.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.102447 restraints weight = 11144.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.107399 restraints weight = 8098.442| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4160 Z= 0.135 Angle : 0.664 8.457 5633 Z= 0.346 Chirality : 0.045 0.176 599 Planarity : 0.005 0.056 718 Dihedral : 8.267 86.456 590 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.86 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.54 (0.36), residues: 490 helix: -0.25 (0.35), residues: 201 sheet: 1.28 (0.74), residues: 43 loop : -0.66 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 30 HIS 0.007 0.001 HIS A 142 PHE 0.042 0.002 PHE A 129 TYR 0.025 0.002 TYR A 247 ARG 0.009 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 169) hydrogen bonds : angle 5.22058 ( 471) covalent geometry : bond 0.00300 ( 4160) covalent geometry : angle 0.66353 ( 5633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6858 (mt) cc_final: 0.6569 (mt) REVERT: A 167 LEU cc_start: 0.8720 (tp) cc_final: 0.8334 (tp) REVERT: A 168 LYS cc_start: 0.9091 (pttt) cc_final: 0.8740 (pttt) REVERT: A 216 ASN cc_start: 0.8912 (p0) cc_final: 0.8612 (p0) REVERT: A 221 TRP cc_start: 0.8955 (m100) cc_final: 0.8246 (m100) REVERT: A 222 TRP cc_start: 0.9085 (t-100) cc_final: 0.8835 (t-100) REVERT: A 231 MET cc_start: 0.9055 (mtm) cc_final: 0.8639 (mmm) REVERT: A 236 PRO cc_start: 0.7942 (Cg_endo) cc_final: 0.7463 (Cg_exo) REVERT: A 324 THR cc_start: 0.8351 (t) cc_final: 0.8105 (m) REVERT: B 94 ARG cc_start: 0.7830 (tmt-80) cc_final: 0.7370 (tmt170) REVERT: B 172 PHE cc_start: 0.9305 (t80) cc_final: 0.8596 (t80) REVERT: B 224 ILE cc_start: 0.9016 (tp) cc_final: 0.8524 (tp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.4189 time to fit residues: 59.0690 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.145763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.088666 restraints weight = 29957.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.096081 restraints weight = 15539.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.101941 restraints weight = 10260.675| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4160 Z= 0.149 Angle : 0.649 7.708 5633 Z= 0.342 Chirality : 0.045 0.182 599 Planarity : 0.005 0.058 718 Dihedral : 7.938 81.395 590 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.27 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -0.13 (0.37), residues: 490 helix: 0.19 (0.36), residues: 200 sheet: 1.09 (0.71), residues: 43 loop : -0.44 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 302 HIS 0.005 0.001 HIS A 142 PHE 0.023 0.002 PHE A 129 TYR 0.021 0.002 TYR A 247 ARG 0.005 0.001 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 169) hydrogen bonds : angle 5.13821 ( 471) covalent geometry : bond 0.00324 ( 4160) covalent geometry : angle 0.64857 ( 5633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6553 (mt) cc_final: 0.6262 (mt) REVERT: A 102 PHE cc_start: 0.8982 (m-80) cc_final: 0.8436 (m-80) REVERT: A 216 ASN cc_start: 0.8762 (p0) cc_final: 0.8237 (m-40) REVERT: A 221 TRP cc_start: 0.8947 (m100) cc_final: 0.8227 (m100) REVERT: A 222 TRP cc_start: 0.9046 (t-100) cc_final: 0.8694 (t-100) REVERT: A 324 THR cc_start: 0.8161 (t) cc_final: 0.7894 (m) REVERT: B 172 PHE cc_start: 0.9314 (t80) cc_final: 0.8676 (t80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2623 time to fit residues: 30.3127 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.140841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081827 restraints weight = 40167.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089820 restraints weight = 18577.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.095816 restraints weight = 11836.326| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4160 Z= 0.188 Angle : 0.691 7.586 5633 Z= 0.357 Chirality : 0.045 0.165 599 Planarity : 0.006 0.064 718 Dihedral : 7.980 79.170 590 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.68 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.37), residues: 490 helix: 0.15 (0.36), residues: 198 sheet: 0.69 (0.76), residues: 38 loop : -0.63 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 302 HIS 0.004 0.001 HIS A 158 PHE 0.028 0.002 PHE A 238 TYR 0.019 0.002 TYR A 215 ARG 0.012 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 169) hydrogen bonds : angle 5.40602 ( 471) covalent geometry : bond 0.00398 ( 4160) covalent geometry : angle 0.69120 ( 5633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.8642 (m-80) cc_final: 0.8249 (m-80) REVERT: A 152 LEU cc_start: 0.9661 (mt) cc_final: 0.9419 (mt) REVERT: A 183 THR cc_start: 0.8690 (t) cc_final: 0.8460 (t) REVERT: A 217 LYS cc_start: 0.8330 (mppt) cc_final: 0.7975 (mmtm) REVERT: A 221 TRP cc_start: 0.8993 (m100) cc_final: 0.8295 (m100) REVERT: A 222 TRP cc_start: 0.9029 (t-100) cc_final: 0.8509 (t-100) REVERT: A 231 MET cc_start: 0.8940 (mtp) cc_final: 0.8304 (mtp) REVERT: A 324 THR cc_start: 0.8118 (t) cc_final: 0.7847 (m) REVERT: B 172 PHE cc_start: 0.9415 (t80) cc_final: 0.8966 (t80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2632 time to fit residues: 29.0568 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.148070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.090925 restraints weight = 26678.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.098750 restraints weight = 14146.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.104124 restraints weight = 9509.559| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4160 Z= 0.123 Angle : 0.651 7.532 5633 Z= 0.338 Chirality : 0.045 0.165 599 Planarity : 0.005 0.071 718 Dihedral : 7.730 83.828 590 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.36), residues: 490 helix: 0.46 (0.36), residues: 192 sheet: 0.38 (0.76), residues: 43 loop : -0.61 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 302 HIS 0.004 0.001 HIS A 142 PHE 0.010 0.001 PHE A 138 TYR 0.016 0.002 TYR A 215 ARG 0.011 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 169) hydrogen bonds : angle 5.08482 ( 471) covalent geometry : bond 0.00273 ( 4160) covalent geometry : angle 0.65059 ( 5633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.8455 (m-80) cc_final: 0.7606 (m-80) REVERT: A 152 LEU cc_start: 0.9669 (mt) cc_final: 0.9437 (mt) REVERT: A 182 VAL cc_start: 0.9255 (p) cc_final: 0.9028 (p) REVERT: A 183 THR cc_start: 0.8555 (t) cc_final: 0.8095 (t) REVERT: A 221 TRP cc_start: 0.8839 (m100) cc_final: 0.8150 (m100) REVERT: A 222 TRP cc_start: 0.8969 (t-100) cc_final: 0.8650 (t-100) REVERT: A 231 MET cc_start: 0.8813 (mtp) cc_final: 0.8418 (mmm) REVERT: A 308 ARG cc_start: 0.8948 (ptm160) cc_final: 0.8610 (mtt90) REVERT: A 324 THR cc_start: 0.8174 (t) cc_final: 0.7910 (m) REVERT: B 172 PHE cc_start: 0.9390 (t80) cc_final: 0.8891 (t80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2637 time to fit residues: 29.6549 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 9 optimal weight: 6.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.089129 restraints weight = 29597.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.096584 restraints weight = 15704.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.102408 restraints weight = 10285.030| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4160 Z= 0.121 Angle : 0.636 7.595 5633 Z= 0.328 Chirality : 0.044 0.150 599 Planarity : 0.005 0.065 718 Dihedral : 7.462 83.834 590 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.04 (0.37), residues: 490 helix: 0.64 (0.38), residues: 193 sheet: 0.44 (0.75), residues: 43 loop : -0.58 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 142 PHE 0.025 0.001 PHE A 238 TYR 0.015 0.001 TYR A 247 ARG 0.005 0.001 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 169) hydrogen bonds : angle 5.05968 ( 471) covalent geometry : bond 0.00276 ( 4160) covalent geometry : angle 0.63561 ( 5633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PHE cc_start: 0.8545 (m-80) cc_final: 0.7655 (m-80) REVERT: A 137 ARG cc_start: 0.6306 (mmp80) cc_final: 0.6065 (mmp80) REVERT: A 152 LEU cc_start: 0.9689 (mt) cc_final: 0.9471 (mt) REVERT: A 183 THR cc_start: 0.8800 (t) cc_final: 0.8368 (t) REVERT: A 217 LYS cc_start: 0.8198 (mppt) cc_final: 0.7000 (mtpt) REVERT: A 221 TRP cc_start: 0.8906 (m100) cc_final: 0.8219 (m100) REVERT: A 222 TRP cc_start: 0.8876 (t-100) cc_final: 0.8618 (t-100) REVERT: A 308 ARG cc_start: 0.8958 (ptm160) cc_final: 0.8667 (mtt90) REVERT: A 324 THR cc_start: 0.8179 (t) cc_final: 0.7901 (m) REVERT: B 111 TYR cc_start: 0.6826 (t80) cc_final: 0.6613 (t80) REVERT: B 172 PHE cc_start: 0.9396 (t80) cc_final: 0.8967 (t80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2462 time to fit residues: 26.0505 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.145692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.084462 restraints weight = 36035.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.093153 restraints weight = 17354.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.099175 restraints weight = 11101.988| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4160 Z= 0.139 Angle : 0.638 8.525 5633 Z= 0.332 Chirality : 0.044 0.160 599 Planarity : 0.005 0.070 718 Dihedral : 7.179 82.079 590 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.89 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.01 (0.38), residues: 490 helix: 0.72 (0.38), residues: 193 sheet: 0.50 (0.78), residues: 43 loop : -0.62 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.004 0.001 HIS A 131 PHE 0.023 0.002 PHE A 257 TYR 0.016 0.002 TYR B 229 ARG 0.004 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 169) hydrogen bonds : angle 5.21914 ( 471) covalent geometry : bond 0.00301 ( 4160) covalent geometry : angle 0.63809 ( 5633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.6666 (mmp80) cc_final: 0.6417 (mmp80) REVERT: A 183 THR cc_start: 0.8848 (t) cc_final: 0.8630 (t) REVERT: A 199 CYS cc_start: 0.4072 (p) cc_final: 0.3294 (p) REVERT: A 217 LYS cc_start: 0.8361 (mppt) cc_final: 0.7119 (mttt) REVERT: A 221 TRP cc_start: 0.8864 (m100) cc_final: 0.8194 (m100) REVERT: A 222 TRP cc_start: 0.8776 (t-100) cc_final: 0.8448 (t-100) REVERT: A 231 MET cc_start: 0.8192 (mmm) cc_final: 0.7325 (mmm) REVERT: A 270 ARG cc_start: 0.8670 (mpt-90) cc_final: 0.8349 (mmt90) REVERT: A 324 THR cc_start: 0.8252 (t) cc_final: 0.7976 (m) REVERT: B 111 TYR cc_start: 0.6788 (t80) cc_final: 0.6496 (t80) REVERT: B 172 PHE cc_start: 0.9305 (t80) cc_final: 0.8949 (t80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2560 time to fit residues: 27.7392 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 44 optimal weight: 0.0050 chunk 46 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.146914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.095194 restraints weight = 16080.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.101056 restraints weight = 10263.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.105520 restraints weight = 7507.121| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.4119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4160 Z= 0.118 Angle : 0.633 8.667 5633 Z= 0.322 Chirality : 0.044 0.160 599 Planarity : 0.005 0.072 718 Dihedral : 6.982 84.426 590 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 0.11 (0.38), residues: 490 helix: 0.82 (0.38), residues: 193 sheet: 0.45 (0.79), residues: 43 loop : -0.53 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 302 HIS 0.005 0.001 HIS A 131 PHE 0.017 0.001 PHE A 238 TYR 0.014 0.001 TYR A 247 ARG 0.004 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 169) hydrogen bonds : angle 5.15304 ( 471) covalent geometry : bond 0.00264 ( 4160) covalent geometry : angle 0.63283 ( 5633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.7046 (mmp80) cc_final: 0.6430 (mmp80) REVERT: A 183 THR cc_start: 0.8417 (t) cc_final: 0.8175 (t) REVERT: A 217 LYS cc_start: 0.8615 (mppt) cc_final: 0.7644 (mttt) REVERT: A 270 ARG cc_start: 0.8690 (mpt-90) cc_final: 0.8318 (mmt90) REVERT: A 324 THR cc_start: 0.8245 (t) cc_final: 0.8003 (m) REVERT: B 94 ARG cc_start: 0.8293 (tmt170) cc_final: 0.8047 (tpt-90) REVERT: B 111 TYR cc_start: 0.6114 (t80) cc_final: 0.5735 (t80) REVERT: B 172 PHE cc_start: 0.9182 (t80) cc_final: 0.8732 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2038 time to fit residues: 21.7009 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.081868 restraints weight = 31626.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.089497 restraints weight = 16068.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.094780 restraints weight = 10741.745| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4160 Z= 0.212 Angle : 0.714 9.897 5633 Z= 0.367 Chirality : 0.046 0.166 599 Planarity : 0.005 0.058 718 Dihedral : 7.243 78.096 590 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.54 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.08 (0.39), residues: 490 helix: 0.62 (0.37), residues: 194 sheet: 0.68 (0.72), residues: 53 loop : -0.48 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 302 HIS 0.006 0.001 HIS A 158 PHE 0.025 0.002 PHE A 185 TYR 0.017 0.002 TYR A 247 ARG 0.004 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 169) hydrogen bonds : angle 5.51332 ( 471) covalent geometry : bond 0.00454 ( 4160) covalent geometry : angle 0.71447 ( 5633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.7394 (mmp80) cc_final: 0.7039 (mmp80) REVERT: A 165 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8483 (ptt180) REVERT: A 205 LEU cc_start: 0.7751 (mm) cc_final: 0.7428 (mm) REVERT: A 217 LYS cc_start: 0.8579 (mppt) cc_final: 0.7439 (mttt) REVERT: A 221 TRP cc_start: 0.8993 (m100) cc_final: 0.8377 (m100) REVERT: A 222 TRP cc_start: 0.8751 (t-100) cc_final: 0.8500 (t-100) REVERT: A 270 ARG cc_start: 0.8609 (mpt-90) cc_final: 0.8258 (mmt90) REVERT: B 111 TYR cc_start: 0.6946 (t80) cc_final: 0.6468 (t80) REVERT: B 172 PHE cc_start: 0.9298 (t80) cc_final: 0.8906 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2150 time to fit residues: 23.0567 Evaluate side-chains 72 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 0.0170 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.141229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.081745 restraints weight = 31259.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.089206 restraints weight = 16693.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.094532 restraints weight = 11476.975| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4160 Z= 0.218 Angle : 0.770 11.154 5633 Z= 0.399 Chirality : 0.047 0.178 599 Planarity : 0.005 0.054 718 Dihedral : 7.439 78.353 590 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.74 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.18 (0.38), residues: 490 helix: 0.49 (0.37), residues: 190 sheet: 0.17 (0.67), residues: 58 loop : -0.61 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 222 HIS 0.004 0.001 HIS A 131 PHE 0.021 0.002 PHE A 185 TYR 0.015 0.002 TYR A 247 ARG 0.010 0.001 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 169) hydrogen bonds : angle 5.90855 ( 471) covalent geometry : bond 0.00470 ( 4160) covalent geometry : angle 0.77035 ( 5633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.7605 (mmp80) cc_final: 0.7222 (mmp80) REVERT: A 205 LEU cc_start: 0.8152 (mm) cc_final: 0.7760 (mm) REVERT: A 217 LYS cc_start: 0.8580 (mppt) cc_final: 0.7446 (mttt) REVERT: A 221 TRP cc_start: 0.8867 (m100) cc_final: 0.8279 (m100) REVERT: A 222 TRP cc_start: 0.8821 (t-100) cc_final: 0.8472 (t-100) REVERT: A 270 ARG cc_start: 0.8639 (mpt-90) cc_final: 0.8259 (mmt90) REVERT: B 111 TYR cc_start: 0.7060 (t80) cc_final: 0.6476 (t80) REVERT: B 172 PHE cc_start: 0.9258 (t80) cc_final: 0.8922 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2069 time to fit residues: 21.2267 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 26 optimal weight: 0.0010 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.095118 restraints weight = 27072.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.102239 restraints weight = 14626.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.107268 restraints weight = 10017.339| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4160 Z= 0.148 Angle : 0.714 10.242 5633 Z= 0.372 Chirality : 0.047 0.150 599 Planarity : 0.005 0.052 718 Dihedral : 7.245 81.510 590 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.54 % Favored : 95.26 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -0.23 (0.39), residues: 490 helix: 0.38 (0.37), residues: 193 sheet: 0.41 (0.71), residues: 53 loop : -0.64 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 302 HIS 0.003 0.001 HIS A 131 PHE 0.015 0.001 PHE A 185 TYR 0.017 0.002 TYR A 247 ARG 0.008 0.001 ARG B 239 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 169) hydrogen bonds : angle 5.72876 ( 471) covalent geometry : bond 0.00332 ( 4160) covalent geometry : angle 0.71373 ( 5633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2616.20 seconds wall clock time: 46 minutes 54.03 seconds (2814.03 seconds total)