Starting phenix.real_space_refine on Thu Jul 24 04:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051.map" model { file = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j09_61051/07_2025/9j09_61051_neut.cif" } resolution = 2.95 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= 0.068 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 149 5.49 5 S 2 5.16 5 C 2735 2.51 5 N 971 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5227 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2053 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 247} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "R" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2440 Classifications: {'RNA': 114} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 7, 'rna3p': 106} Chain breaks: 4 Time building chain proxies: 11.20, per 1000 atoms: 2.14 Number of scatterers: 5227 At special positions: 0 Unit cell: (87.36, 97.92, 90.24, 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 2 16.00 P 149 15.00 O 1370 8.00 N 971 7.00 C 2735 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: 1.96 Conformation dependent library (CDL) restraints added in 701.5 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 484 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 51.4% alpha, 12.5% beta 46 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 63 removed outlier: 3.865A pdb=" N ALA A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 80 removed outlier: 4.150A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 6.906A pdb=" N ARG A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.717A pdb=" N GLU A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.713A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 161 removed outlier: 3.746A pdb=" N GLY A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.709A pdb=" N ARG A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG A 253 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR A 259 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 251 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 261 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 249 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 263 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 265 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 245 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 104 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 4.04 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 553 1.32 - 1.44: 2385 1.44 - 1.56: 2417 1.56 - 1.68: 292 1.68 - 1.80: 4 Bond restraints: 5651 Sorted by residual: bond pdb=" C ILE A 227 " pdb=" O ILE A 227 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.05e-02 9.07e+03 1.34e+01 bond pdb=" O5' U R -3 " pdb=" C5' U R -3 " ideal model delta sigma weight residual 1.420 1.466 -0.046 1.50e-02 4.44e+03 9.32e+00 bond pdb=" O5' G R -6 " pdb=" C5' G R -6 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.57e+00 bond pdb=" N SER A 222 " pdb=" CA SER A 222 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.42e+00 bond pdb=" P U R -4 " pdb=" O5' U R -4 " ideal model delta sigma weight residual 1.593 1.629 -0.036 1.50e-02 4.44e+03 5.83e+00 ... (remaining 5646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 8138 4.13 - 8.26: 200 8.26 - 12.40: 9 12.40 - 16.53: 2 16.53 - 20.66: 1 Bond angle restraints: 8350 Sorted by residual: angle pdb=" O3' U R 4 " pdb=" P C R 5 " pdb=" O5' C R 5 " ideal model delta sigma weight residual 104.00 124.66 -20.66 1.50e+00 4.44e-01 1.90e+02 angle pdb=" O4' C R 0 " pdb=" C1' C R 0 " pdb=" C2' C R 0 " ideal model delta sigma weight residual 105.80 99.15 6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" C3' U R 3 " pdb=" C2' U R 3 " pdb=" O2' U R 3 " ideal model delta sigma weight residual 110.70 120.08 -9.38 1.50e+00 4.44e-01 3.91e+01 angle pdb=" O2' U R 3 " pdb=" C2' U R 3 " pdb=" C1' U R 3 " ideal model delta sigma weight residual 108.40 99.15 9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" O3' U R 3 " pdb=" C3' U R 3 " pdb=" C2' U R 3 " ideal model delta sigma weight residual 113.70 122.85 -9.15 1.50e+00 4.44e-01 3.72e+01 ... (remaining 8345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 2826 33.25 - 66.50: 508 66.50 - 99.75: 52 99.75 - 133.01: 3 133.01 - 166.26: 1 Dihedral angle restraints: 3390 sinusoidal: 2634 harmonic: 756 Sorted by residual: dihedral pdb=" O4' C R -68 " pdb=" C1' C R -68 " pdb=" N1 C R -68 " pdb=" C2 C R -68 " ideal model delta sinusoidal sigma weight residual 200.00 33.74 166.26 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" C5' A R-152 " pdb=" C4' A R-152 " pdb=" C3' A R-152 " pdb=" O3' A R-152 " ideal model delta sinusoidal sigma weight residual 147.00 102.98 44.02 1 8.00e+00 1.56e-02 4.21e+01 dihedral pdb=" O4' G R-145 " pdb=" C2' G R-145 " pdb=" C1' G R-145 " pdb=" C3' G R-145 " ideal model delta sinusoidal sigma weight residual 25.00 -17.70 42.70 1 8.00e+00 1.56e-02 3.98e+01 ... (remaining 3387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 904 0.143 - 0.285: 45 0.285 - 0.428: 7 0.428 - 0.571: 37 0.571 - 0.714: 18 Chirality restraints: 1011 Sorted by residual: chirality pdb=" P DC D -11 " pdb=" OP1 DC D -11 " pdb=" OP2 DC D -11 " pdb=" O5' DC D -11 " both_signs ideal model delta sigma weight residual True 2.35 -3.06 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" P C R 0 " pdb=" OP1 C R 0 " pdb=" OP2 C R 0 " pdb=" O5' C R 0 " both_signs ideal model delta sigma weight residual True 2.41 -3.10 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" P G R 10 " pdb=" OP1 G R 10 " pdb=" OP2 G R 10 " pdb=" O5' G R 10 " both_signs ideal model delta sigma weight residual True 2.41 -3.10 -0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1008 not shown) Planarity restraints: 519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 27 " -0.052 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 DG C 27 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DG C 27 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 27 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG C 27 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG C 27 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG C 27 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG C 27 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG C 27 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " 0.024 2.00e-02 2.50e+03 1.41e-02 5.95e+00 pdb=" N9 DG C 17 " -0.035 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 4 " -0.029 2.00e-02 2.50e+03 1.48e-02 4.96e+00 pdb=" N1 U R 4 " 0.028 2.00e-02 2.50e+03 pdb=" C2 U R 4 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U R 4 " 0.009 2.00e-02 2.50e+03 pdb=" N3 U R 4 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U R 4 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U R 4 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U R 4 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U R 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 516 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 119 2.61 - 3.18: 4028 3.18 - 3.76: 9633 3.76 - 4.33: 12155 4.33 - 4.90: 17212 Nonbonded interactions: 43147 Sorted by model distance: nonbonded pdb=" O2' A R -55 " pdb=" O4' U R -54 " model vdw 2.040 3.040 nonbonded pdb=" OD2 ASP A 117 " pdb=" OG SER A 119 " model vdw 2.271 3.040 nonbonded pdb=" O2' C R -94 " pdb=" O4 U R -57 " model vdw 2.283 3.040 nonbonded pdb=" O2 U R -41 " pdb=" N2 G R -10 " model vdw 2.335 2.496 nonbonded pdb=" NH1 ARG A 253 " pdb=" O ALA A 255 " model vdw 2.362 3.120 ... (remaining 43142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 301.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 30.820 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:22.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 355.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4548 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 : 0.008 0.047 5651 Z= 0.422 Angle : 1.363 20.659 8350 Z= 0.720 Chirality : 0.144 0.714 1011 Planarity : 0.005 0.050 519 Dihedral : 26.407 166.258 2906 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 4.95 % Allowed : 1.98 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.40 (0.52), residues: 255 helix: 1.25 (0.47), residues: 121 sheet: -0.19 (0.83), residues: 41 loop : -2.42 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 153 HIS 0.015 0.004 HIS A 110 PHE 0.011 0.002 PHE A 156 TYR 0.015 0.002 TYR A 195 ARG 0.003 0.000 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.18463 ( 216) hydrogen bonds : angle 9.15292 ( 512) covalent geometry : bond 0.00785 ( 5651) covalent geometry : angle 1.36291 ( 8350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.461 Fit side-chains REVERT: A 11 ASN cc_start: 0.7118 (p0) cc_final: 0.6893 (p0) REVERT: A 97 TYR cc_start: 0.5966 (m-80) cc_final: 0.5723 (m-80) REVERT: A 104 ARG cc_start: 0.4942 (ttp80) cc_final: 0.4389 (mtm110) REVERT: A 106 GLU cc_start: 0.4706 (tt0) cc_final: 0.3879 (tp30) REVERT: A 176 LYS cc_start: 0.7044 (mttp) cc_final: 0.6755 (mttp) REVERT: A 181 ARG cc_start: 0.3146 (mtp180) cc_final: 0.1434 (ptp90) REVERT: A 191 LYS cc_start: 0.6689 (tppp) cc_final: 0.4732 (pmtt) outliers start: 10 outliers final: 1 residues processed: 34 average time/residue: 3.5971 time to fit residues: 126.0573 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.0030 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.268813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.243113 restraints weight = 4390.788| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 0.60 r_work: 0.4394 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5651 Z= 0.196 Angle : 0.764 5.983 8350 Z= 0.405 Chirality : 0.042 0.272 1011 Planarity : 0.006 0.047 519 Dihedral : 26.688 178.765 2435 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 2.97 % Allowed : 7.92 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.32 (0.54), residues: 255 helix: 1.71 (0.48), residues: 118 sheet: -1.05 (0.77), residues: 49 loop : -2.46 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 153 HIS 0.003 0.001 HIS A 135 PHE 0.011 0.002 PHE A 156 TYR 0.020 0.002 TYR A 195 ARG 0.004 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.07837 ( 216) hydrogen bonds : angle 4.12559 ( 512) covalent geometry : bond 0.00389 ( 5651) covalent geometry : angle 0.76415 ( 8350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.324 Fit side-chains REVERT: A 104 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7502 (mtm110) REVERT: A 106 GLU cc_start: 0.6789 (tt0) cc_final: 0.6523 (tp30) outliers start: 6 outliers final: 2 residues processed: 21 average time/residue: 1.4173 time to fit residues: 31.2102 Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0050 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.272107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.235502 restraints weight = 4271.569| |-----------------------------------------------------------------------------| r_work (start): 0.4702 rms_B_bonded: 1.02 r_work: 0.4251 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5651 Z= 0.205 Angle : 0.737 7.083 8350 Z= 0.393 Chirality : 0.042 0.275 1011 Planarity : 0.006 0.051 519 Dihedral : 26.273 178.371 2435 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.80 % Rotamer: Outliers : 2.97 % Allowed : 12.87 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.61 (0.52), residues: 255 helix: 1.48 (0.47), residues: 119 sheet: -1.36 (0.75), residues: 49 loop : -2.53 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 153 HIS 0.004 0.002 HIS A 218 PHE 0.013 0.002 PHE A 156 TYR 0.019 0.002 TYR A 195 ARG 0.008 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.07640 ( 216) hydrogen bonds : angle 4.12636 ( 512) covalent geometry : bond 0.00416 ( 5651) covalent geometry : angle 0.73712 ( 8350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5728 (tp) REVERT: A 49 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: A 104 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7470 (mtp85) REVERT: A 106 GLU cc_start: 0.6943 (tt0) cc_final: 0.6698 (tp30) REVERT: A 133 TRP cc_start: 0.6756 (p-90) cc_final: 0.5472 (p-90) outliers start: 6 outliers final: 2 residues processed: 21 average time/residue: 1.5300 time to fit residues: 33.4922 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.267991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.229301 restraints weight = 4387.531| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 1.10 r_work: 0.4175 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5651 Z= 0.234 Angle : 0.776 7.843 8350 Z= 0.411 Chirality : 0.043 0.234 1011 Planarity : 0.007 0.045 519 Dihedral : 26.316 177.957 2433 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.02 % Favored : 90.59 % Rotamer: Outliers : 2.48 % Allowed : 14.85 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.92 (0.51), residues: 255 helix: 1.29 (0.46), residues: 117 sheet: -1.56 (0.72), residues: 49 loop : -2.67 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 153 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.002 PHE A 156 TYR 0.019 0.003 TYR A 195 ARG 0.007 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.08355 ( 216) hydrogen bonds : angle 4.25188 ( 512) covalent geometry : bond 0.00482 ( 5651) covalent geometry : angle 0.77565 ( 8350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.314 Fit side-chains REVERT: A 104 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7645 (mtp85) REVERT: A 106 GLU cc_start: 0.6885 (tt0) cc_final: 0.6652 (tp30) REVERT: A 133 TRP cc_start: 0.6828 (p-90) cc_final: 0.5543 (p-90) REVERT: A 139 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.6163 (mm-40) outliers start: 5 outliers final: 1 residues processed: 20 average time/residue: 1.7008 time to fit residues: 35.3368 Evaluate side-chains 18 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.272956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.239271 restraints weight = 4332.693| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 0.90 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5651 Z= 0.164 Angle : 0.657 6.237 8350 Z= 0.353 Chirality : 0.038 0.186 1011 Planarity : 0.005 0.036 519 Dihedral : 26.035 174.640 2433 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 1.98 % Allowed : 17.33 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.40 (0.53), residues: 255 helix: 1.80 (0.47), residues: 119 sheet: -1.52 (0.74), residues: 49 loop : -2.49 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 153 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE A 156 TYR 0.016 0.002 TYR A 195 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.06421 ( 216) hydrogen bonds : angle 3.91447 ( 512) covalent geometry : bond 0.00332 ( 5651) covalent geometry : angle 0.65661 ( 8350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.308 Fit side-chains REVERT: A 104 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7636 (mtm110) REVERT: A 133 TRP cc_start: 0.6651 (p-90) cc_final: 0.5602 (p-90) outliers start: 4 outliers final: 0 residues processed: 20 average time/residue: 1.6174 time to fit residues: 33.6607 Evaluate side-chains 16 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.268075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.229886 restraints weight = 4297.345| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 1.05 r_work: 0.4162 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5651 Z= 0.234 Angle : 0.758 6.796 8350 Z= 0.400 Chirality : 0.042 0.214 1011 Planarity : 0.006 0.044 519 Dihedral : 26.150 177.962 2433 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 3.47 % Allowed : 17.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.52), residues: 255 helix: 1.47 (0.47), residues: 117 sheet: -1.65 (0.72), residues: 49 loop : -2.58 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 153 HIS 0.003 0.001 HIS A 105 PHE 0.013 0.002 PHE A 156 TYR 0.020 0.002 TYR A 195 ARG 0.005 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.08042 ( 216) hydrogen bonds : angle 4.09947 ( 512) covalent geometry : bond 0.00484 ( 5651) covalent geometry : angle 0.75789 ( 8350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.336 Fit side-chains REVERT: A 104 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7492 (mtm110) REVERT: A 106 GLU cc_start: 0.6901 (tp30) cc_final: 0.6648 (tt0) outliers start: 7 outliers final: 3 residues processed: 23 average time/residue: 1.7084 time to fit residues: 40.8766 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 0.1980 chunk 36 optimal weight: 6.9990 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.276689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.257750 restraints weight = 4295.886| |-----------------------------------------------------------------------------| r_work (start): 0.4916 rms_B_bonded: 0.55 r_work: 0.4654 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.4577 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5651 Z= 0.141 Angle : 0.627 6.595 8350 Z= 0.339 Chirality : 0.035 0.170 1011 Planarity : 0.005 0.036 519 Dihedral : 25.882 173.826 2433 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.84 % Favored : 91.76 % Rotamer: Outliers : 1.49 % Allowed : 19.31 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.05 (0.54), residues: 255 helix: 2.10 (0.48), residues: 119 sheet: -1.43 (0.76), residues: 49 loop : -2.30 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 153 HIS 0.011 0.002 HIS A 105 PHE 0.011 0.001 PHE A 156 TYR 0.014 0.001 TYR A 195 ARG 0.002 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05564 ( 216) hydrogen bonds : angle 3.78607 ( 512) covalent geometry : bond 0.00286 ( 5651) covalent geometry : angle 0.62731 ( 8350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.322 Fit side-chains REVERT: A 104 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7567 (mtm110) outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 1.6746 time to fit residues: 34.8921 Evaluate side-chains 17 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.266121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.228810 restraints weight = 4287.109| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.09 r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5651 Z= 0.293 Angle : 0.848 7.711 8350 Z= 0.442 Chirality : 0.046 0.245 1011 Planarity : 0.007 0.056 519 Dihedral : 26.244 179.190 2433 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 2.97 % Allowed : 17.82 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.51), residues: 255 helix: 1.10 (0.47), residues: 117 sheet: -1.74 (0.73), residues: 49 loop : -2.52 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 153 HIS 0.004 0.002 HIS A 135 PHE 0.014 0.003 PHE A 156 TYR 0.023 0.003 TYR A 195 ARG 0.006 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.09151 ( 216) hydrogen bonds : angle 4.30433 ( 512) covalent geometry : bond 0.00610 ( 5651) covalent geometry : angle 0.84752 ( 8350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.329 Fit side-chains REVERT: A 49 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6207 (tm-30) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 1.3912 time to fit residues: 32.0500 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.270443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.253186 restraints weight = 4261.080| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 0.54 r_work: 0.4605 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.4553 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5651 Z= 0.190 Angle : 0.701 6.720 8350 Z= 0.375 Chirality : 0.039 0.186 1011 Planarity : 0.006 0.038 519 Dihedral : 26.034 176.816 2433 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.24 % Favored : 91.37 % Rotamer: Outliers : 2.48 % Allowed : 18.32 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.71 (0.52), residues: 255 helix: 1.39 (0.47), residues: 120 sheet: -1.69 (0.74), residues: 49 loop : -2.43 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 153 HIS 0.007 0.002 HIS A 105 PHE 0.012 0.002 PHE A 156 TYR 0.017 0.002 TYR A 195 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.06912 ( 216) hydrogen bonds : angle 4.01316 ( 512) covalent geometry : bond 0.00389 ( 5651) covalent geometry : angle 0.70081 ( 8350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.334 Fit side-chains REVERT: A 104 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7706 (mtp85) outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 1.6090 time to fit residues: 36.8355 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.268460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.236139 restraints weight = 4319.570| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 0.92 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5651 Z= 0.224 Angle : 0.744 6.781 8350 Z= 0.394 Chirality : 0.041 0.205 1011 Planarity : 0.006 0.043 519 Dihedral : 26.053 177.728 2433 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.20 % Favored : 89.41 % Rotamer: Outliers : 1.49 % Allowed : 18.81 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.89 (0.51), residues: 255 helix: 1.33 (0.47), residues: 118 sheet: -1.85 (0.72), residues: 49 loop : -2.51 (0.55), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 153 HIS 0.003 0.001 HIS A 110 PHE 0.014 0.002 PHE A 156 TYR 0.019 0.002 TYR A 195 ARG 0.005 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.07804 ( 216) hydrogen bonds : angle 4.08051 ( 512) covalent geometry : bond 0.00463 ( 5651) covalent geometry : angle 0.74412 ( 8350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.338 Fit side-chains REVERT: A 104 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7744 (mtp85) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 1.5798 time to fit residues: 34.5842 Evaluate side-chains 20 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.268151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.250704 restraints weight = 4324.120| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 0.54 r_work: 0.4605 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.4555 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5651 Z= 0.227 Angle : 0.749 6.817 8350 Z= 0.397 Chirality : 0.042 0.207 1011 Planarity : 0.006 0.043 519 Dihedral : 26.053 177.735 2433 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.80 % Favored : 89.80 % Rotamer: Outliers : 2.48 % Allowed : 17.82 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.94 (0.51), residues: 255 helix: 1.25 (0.47), residues: 118 sheet: -1.87 (0.72), residues: 49 loop : -2.48 (0.55), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 153 HIS 0.005 0.002 HIS A 110 PHE 0.013 0.002 PHE A 156 TYR 0.020 0.002 TYR A 195 ARG 0.005 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.07793 ( 216) hydrogen bonds : angle 4.09075 ( 512) covalent geometry : bond 0.00472 ( 5651) covalent geometry : angle 0.74887 ( 8350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.90 seconds wall clock time: 71 minutes 6.01 seconds (4266.01 seconds total)