Starting phenix.real_space_refine on Tue Feb 11 03:27:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.map" model { file = "/net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7efd_31084/02_2025/7efd_31084.cif" } resolution = 1.77 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= 0.007 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 946 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 120, 896 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} bond proxies already assigned to first conformer: 867 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 40, 55 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1, 'water': 39} Link IDs: {None: 39} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Restraints were copied for chains: C, B, D Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5225 " occ=0.50 residue: pdb=" O AHOH A5226 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 2.74, per 1000 atoms: 0.68 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 940 8.00 N 668 7.00 C 2392 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: 1.00 Conformation dependent library (CDL) restraints added in 931.5 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 5.8% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 540 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: 1.19 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 540 1.28 - 1.42: 876 1.42 - 1.55: 2196 1.55 - 1.68: 324 1.68 - 1.82: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C THR A 42 " pdb=" O THR A 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR B 42 " pdb=" O THR B 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR D 42 " pdb=" O THR D 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR C 42 " pdb=" O THR C 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.313 -0.082 1.05e-02 9.07e+03 6.03e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 3452 2.76 - 5.51: 1456 5.51 - 8.26: 432 8.26 - 11.01: 40 11.01 - 13.77: 20 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.32 10.53 1.06e+00 8.90e-01 9.87e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.60: 2012 16.60 - 33.19: 148 33.19 - 49.79: 28 49.79 - 66.38: 12 66.38 - 82.98: 12 Dihedral angle restraints: 2212 sinusoidal: 788 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER C 52 " pdb=" C ASER C 52 " pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 424 0.083 - 0.166: 152 0.166 - 0.248: 20 0.248 - 0.331: 0 0.331 - 0.414: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL D 125 " pdb=" CA VAL D 125 " pdb=" CG1 VAL D 125 " pdb=" CG2 VAL D 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL C 125 " pdb=" CA VAL C 125 " pdb=" CG1 VAL C 125 " pdb=" CG2 VAL C 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN D5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN D5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN D5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN D5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN D5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN D5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN B5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN A5100 " 0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.245 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1410 2.94 - 3.92: 11570 3.92 - 4.90: 22800 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35782 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 3.040 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN B 49 " pdb=" OD1AASN B 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.212 3.040 ... (remaining 35777 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.94 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: 0.200 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: 0.040 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.033 0.119 3944 Z= 2.153 Angle : 3.163 13.767 5400 Z= 2.200 Chirality : 0.091 0.414 604 Planarity : 0.015 0.201 684 Dihedral : 15.318 82.977 1324 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.85 % Allowed : 1.69 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 2.70 % 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 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.31), residues: 224 loop : -1.12 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 92 HIS 0.001 0.000 HIS B 127 PHE 0.002 0.001 PHE C 130 TYR 0.002 0.001 TYR D 60 ARG 0.000 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8196 (m) cc_final: 0.7701 (p) REVERT: A 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: B 27 SER cc_start: 0.8197 (m) cc_final: 0.7701 (p) REVERT: B 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7455 (ttp80) REVERT: C 27 SER cc_start: 0.8195 (m) cc_final: 0.7701 (p) REVERT: C 103 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: D 27 SER cc_start: 0.8197 (m) cc_final: 0.7702 (p) REVERT: D 103 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7454 (ttp80) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.4479 time to fit residues: 95.3543 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 118 ASN B 107 GLN B 118 ASN C 107 GLN C 118 ASN D 107 GLN D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152492 restraints weight = 7014.682| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.66 r_work: 0.3746 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.162 3944 Z= 0.722 Angle : 1.700 22.900 5400 Z= 0.930 Chirality : 0.081 0.397 604 Planarity : 0.021 0.380 684 Dihedral : 9.903 59.927 636 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.75 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 10.48 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.32 (0.34), residues: 512 helix: -4.64 (0.24), residues: 24 sheet: 0.02 (0.27), residues: 264 loop : -1.49 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.009 TRP B 108 HIS 0.008 0.003 HIS C 87 PHE 0.119 0.019 PHE B 29 TYR 0.284 0.016 TYR C 43 ARG 0.157 0.010 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 68 average time/residue: 1.3538 time to fit residues: 94.9001 Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154090 restraints weight = 3804.737| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.24 r_work: 0.3702 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3944 Z= 0.287 Angle : 0.801 8.902 5400 Z= 0.433 Chirality : 0.046 0.155 604 Planarity : 0.005 0.062 684 Dihedral : 7.492 46.307 632 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer: Outliers : 0.27 % Allowed : 10.75 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.40 (0.25), residues: 300 loop : 0.41 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 75 HIS 0.005 0.002 HIS C 87 PHE 0.024 0.004 PHE A 29 TYR 0.014 0.003 TYR B 22 ARG 0.005 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7505 (ttp80) REVERT: C 53 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7536 (ttp80) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 1.5106 time to fit residues: 103.9525 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154552 restraints weight = 4340.500| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.22 r_work: 0.3784 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3944 Z= 0.234 Angle : 0.706 9.126 5400 Z= 0.383 Chirality : 0.045 0.153 604 Planarity : 0.004 0.040 684 Dihedral : 7.114 46.920 632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.18 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 10.75 % Favored : 88.98 % 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: 0.90 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.72 (0.25), residues: 292 loop : 0.61 (0.50), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 92 HIS 0.004 0.002 HIS C 87 PHE 0.026 0.004 PHE B 29 TYR 0.015 0.002 TYR B 22 ARG 0.003 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 1.5490 time to fit residues: 101.8129 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154676 restraints weight = 4321.461| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.32 r_work: 0.3777 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.203 Angle : 0.653 7.068 5400 Z= 0.357 Chirality : 0.043 0.151 604 Planarity : 0.003 0.016 684 Dihedral : 6.960 43.868 632 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.60 % Favored : 95.76 % Rotamer: Outliers : 0.27 % Allowed : 10.75 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.82 (0.26), residues: 292 loop : 0.71 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 92 HIS 0.004 0.001 HIS C 87 PHE 0.019 0.003 PHE B 29 TYR 0.012 0.002 TYR B 22 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 1.5553 time to fit residues: 108.5952 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.174240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.155598 restraints weight = 3573.006| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 0.98 r_work: 0.3764 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3944 Z= 0.390 Angle : 0.800 5.236 5400 Z= 0.445 Chirality : 0.049 0.157 604 Planarity : 0.006 0.038 684 Dihedral : 7.552 49.728 632 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.60 % Favored : 95.55 % Rotamer: Outliers : 0.81 % Allowed : 10.48 % Favored : 88.71 % 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: 0.79 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.73 (0.25), residues: 292 loop : 0.39 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 92 HIS 0.006 0.003 HIS C 87 PHE 0.020 0.004 PHE B 29 TYR 0.014 0.004 TYR A 22 ARG 0.006 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 1.6757 time to fit residues: 115.0917 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.177190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.155940 restraints weight = 4101.237| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.25 r_work: 0.3792 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3944 Z= 0.175 Angle : 0.617 6.122 5400 Z= 0.338 Chirality : 0.043 0.156 604 Planarity : 0.003 0.015 684 Dihedral : 6.882 45.225 632 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.97 % Favored : 96.61 % Rotamer: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.17 % 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: 0.96 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.75 (0.26), residues: 296 loop : 0.66 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.012 0.002 PHE C 29 TYR 0.011 0.002 TYR D 22 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 1.5674 time to fit residues: 109.3808 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155819 restraints weight = 3643.113| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 0.98 r_work: 0.3808 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.204 Angle : 0.645 6.890 5400 Z= 0.352 Chirality : 0.043 0.156 604 Planarity : 0.003 0.017 684 Dihedral : 6.956 46.016 632 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.86 (0.26), residues: 292 loop : 0.59 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.012 0.003 PHE C 29 TYR 0.012 0.002 TYR A 22 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 1.5872 time to fit residues: 115.7351 Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.175157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151289 restraints weight = 4372.789| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.19 r_work: 0.3765 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.189 Angle : 0.634 7.642 5400 Z= 0.343 Chirality : 0.043 0.159 604 Planarity : 0.003 0.016 684 Dihedral : 6.848 45.394 632 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.78 (0.26), residues: 296 loop : 0.77 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 92 HIS 0.003 0.001 HIS C 87 PHE 0.009 0.002 PHE C 29 TYR 0.012 0.002 TYR A 22 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.5867 time to fit residues: 109.0156 Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.173253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149551 restraints weight = 4042.102| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.16 r_work: 0.3744 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3944 Z= 0.301 Angle : 0.721 6.029 5400 Z= 0.397 Chirality : 0.048 0.211 604 Planarity : 0.004 0.026 684 Dihedral : 7.230 48.391 632 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.70 (0.26), residues: 296 loop : 0.58 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 92 HIS 0.005 0.002 HIS C 87 PHE 0.007 0.002 PHE D 29 TYR 0.014 0.003 TYR D 22 ARG 0.004 0.001 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 1.8563 time to fit residues: 123.6525 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.171973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.148406 restraints weight = 3848.670| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.11 r_work: 0.3720 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3944 Z= 0.337 Angle : 0.753 6.345 5400 Z= 0.416 Chirality : 0.048 0.195 604 Planarity : 0.005 0.031 684 Dihedral : 7.312 49.079 632 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.39 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.68 (0.26), residues: 296 loop : 0.43 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 92 HIS 0.006 0.002 HIS C 87 PHE 0.010 0.003 PHE D 29 TYR 0.015 0.003 TYR A 22 ARG 0.005 0.001 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4698.22 seconds wall clock time: 83 minutes 19.60 seconds (4999.60 seconds total)