Starting phenix.real_space_refine on Wed Sep 17 05:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.map" model { file = "/net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dm7_46999/09_2025/9dm7_46999.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 428 atoms to isotropic. 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 16 5.16 5 C 3051 2.51 5 N 772 2.21 5 O 807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2870 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 973 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.38, per 1000 atoms: 0.30 Number of scatterers: 4646 At special positions: 0 Unit cell: (100.05, 79.17, 94.83, 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 16 16.00 O 807 8.00 N 772 7.00 C 3051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 0.43 Conformation dependent library (CDL) restraints added in 188.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1082 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 50.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 4.022A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.773A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.600A pdb=" N ALA A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 107 through 135 removed outlier: 3.892A pdb=" N ILE A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.766A pdb=" N LEU A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.802A pdb=" N VAL A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 4.008A pdb=" N TYR A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.577A pdb=" N VAL A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 removed outlier: 4.513A pdb=" N TYR A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.593A pdb=" N THR A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.359A pdb=" N VAL A 324 " --> pdb=" O HIS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.815A pdb=" N PHE A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.333A pdb=" N ASP A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 384 through 404 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.647A pdb=" N TYR H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.595A pdb=" N ASN H 77 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.660A pdb=" N THR H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER H 50 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 101 through 105 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.830A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.615A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.57 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: 717 1.32 - 1.45: 1468 1.45 - 1.57: 2578 1.57 - 1.69: 0 1.69 - 1.82: 25 Bond restraints: 4788 Sorted by residual: bond pdb=" C VAL A 285 " pdb=" O VAL A 285 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.35e-02 5.49e+03 7.89e+00 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.59e-02 3.96e+03 6.12e+00 bond pdb=" CA ALA A 284 " pdb=" CB ALA A 284 " ideal model delta sigma weight residual 1.530 1.491 0.038 1.56e-02 4.11e+03 6.02e+00 bond pdb=" C ASP A 58 " pdb=" N LEU A 59 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.38e-02 5.25e+03 5.35e+00 bond pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.83e+00 ... (remaining 4783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6362 1.72 - 3.44: 142 3.44 - 5.16: 36 5.16 - 6.88: 5 6.88 - 8.60: 4 Bond angle restraints: 6549 Sorted by residual: angle pdb=" C GLN L 27 " pdb=" CA GLN L 27 " pdb=" CB GLN L 27 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.84e+01 angle pdb=" C PRO A 33 " pdb=" N TRP A 34 " pdb=" CA TRP A 34 " ideal model delta sigma weight residual 121.66 113.06 8.60 1.76e+00 3.23e-01 2.39e+01 angle pdb=" C TRP A 211 " pdb=" N THR A 212 " pdb=" CA THR A 212 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" N VAL A 342 " pdb=" CA VAL A 342 " pdb=" C VAL A 342 " ideal model delta sigma weight residual 111.91 108.35 3.56 8.90e-01 1.26e+00 1.60e+01 angle pdb=" CA ALA A 284 " pdb=" C ALA A 284 " pdb=" O ALA A 284 " ideal model delta sigma weight residual 120.90 117.19 3.71 1.07e+00 8.73e-01 1.21e+01 ... (remaining 6544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 2435 16.11 - 32.22: 189 32.22 - 48.33: 49 48.33 - 64.44: 9 64.44 - 80.55: 3 Dihedral angle restraints: 2685 sinusoidal: 985 harmonic: 1700 Sorted by residual: dihedral pdb=" CA ARG A 132 " pdb=" CB ARG A 132 " pdb=" CG ARG A 132 " pdb=" CD ARG A 132 " ideal model delta sinusoidal sigma weight residual -180.00 -121.66 -58.34 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA SER L 12 " pdb=" C SER L 12 " pdb=" N ALA L 13 " pdb=" CA ALA L 13 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.43e+00 dihedral pdb=" CA ASP A 299 " pdb=" CB ASP A 299 " pdb=" CG ASP A 299 " pdb=" OD1 ASP A 299 " ideal model delta sinusoidal sigma weight residual -30.00 -82.14 52.14 1 2.00e+01 2.50e-03 9.27e+00 ... (remaining 2682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 479 0.033 - 0.065: 174 0.065 - 0.098: 55 0.098 - 0.131: 23 0.131 - 0.164: 6 Chirality restraints: 737 Sorted by residual: chirality pdb=" CB VAL A 232 " pdb=" CA VAL A 232 " pdb=" CG1 VAL A 232 " pdb=" CG2 VAL A 232 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CB VAL A 285 " pdb=" CA VAL A 285 " pdb=" CG1 VAL A 285 " pdb=" CG2 VAL A 285 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA TRP A 377 " pdb=" N TRP A 377 " pdb=" C TRP A 377 " pdb=" CB TRP A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 734 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " 0.038 2.00e-02 2.50e+03 1.77e-02 7.80e+00 pdb=" CG TRP A 34 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 212 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C THR A 212 " 0.040 2.00e-02 2.50e+03 pdb=" O THR A 212 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 213 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO H 41 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.031 5.00e-02 4.00e+02 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 6 2.32 - 2.97: 2168 2.97 - 3.61: 6470 3.61 - 4.26: 9603 4.26 - 4.90: 16982 Nonbonded interactions: 35229 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" O GLN L 100 " model vdw 1.675 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" NE2 GLN A 163 " model vdw 2.135 3.120 nonbonded pdb=" OH TYR H 60 " pdb=" O ARG H 67 " model vdw 2.170 3.040 nonbonded pdb=" O GLU L 81 " pdb=" NZ LYS L 103 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR H 30 " model vdw 2.285 3.040 ... (remaining 35224 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.003 0.039 4790 Z= 0.182 Angle : 0.674 8.605 6553 Z= 0.385 Chirality : 0.042 0.164 737 Planarity : 0.005 0.055 793 Dihedral : 12.690 80.553 1597 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.36), residues: 584 helix: 1.41 (0.33), residues: 275 sheet: -1.10 (0.58), residues: 90 loop : -3.08 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.008 0.001 TYR A 75 PHE 0.013 0.001 PHE H 68 TRP 0.038 0.001 TRP A 34 HIS 0.002 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4788) covalent geometry : angle 0.67354 ( 6549) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.13092 ( 4) hydrogen bonds : bond 0.17084 ( 222) hydrogen bonds : angle 6.41161 ( 630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.160 Fit side-chains REVERT: L 3 GLN cc_start: 0.7131 (mp-120) cc_final: 0.6866 (mp10) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0810 time to fit residues: 6.3490 Evaluate side-chains 53 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.188413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.168276 restraints weight = 5825.570| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.65 r_work: 0.3749 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4790 Z= 0.148 Angle : 0.628 7.302 6553 Z= 0.319 Chirality : 0.043 0.167 737 Planarity : 0.005 0.044 793 Dihedral : 4.155 18.323 646 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.66 % Allowed : 5.80 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.35), residues: 584 helix: 1.49 (0.32), residues: 277 sheet: -0.57 (0.56), residues: 98 loop : -3.39 (0.34), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.012 0.001 TYR H 112 PHE 0.008 0.001 PHE H 68 TRP 0.012 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4788) covalent geometry : angle 0.62580 ( 6549) SS BOND : bond 0.00986 ( 2) SS BOND : angle 2.26641 ( 4) hydrogen bonds : bond 0.05171 ( 222) hydrogen bonds : angle 4.58810 ( 630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.182 Fit side-chains REVERT: A 209 ARG cc_start: 0.7052 (tpp-160) cc_final: 0.6777 (tpp80) REVERT: A 384 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6862 (mp) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.0812 time to fit residues: 5.8326 Evaluate side-chains 54 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.0020 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.192505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.172513 restraints weight = 5745.152| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.69 r_work: 0.3793 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 4790 Z= 0.110 Angle : 0.558 5.875 6553 Z= 0.284 Chirality : 0.040 0.151 737 Planarity : 0.004 0.041 793 Dihedral : 3.915 17.086 646 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.66 % Allowed : 8.07 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.36), residues: 584 helix: 1.77 (0.32), residues: 278 sheet: -0.01 (0.62), residues: 82 loop : -3.25 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.009 0.001 TYR H 112 PHE 0.007 0.001 PHE H 68 TRP 0.011 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4788) covalent geometry : angle 0.55687 ( 6549) SS BOND : bond 0.00664 ( 2) SS BOND : angle 1.49570 ( 4) hydrogen bonds : bond 0.03766 ( 222) hydrogen bonds : angle 4.16616 ( 630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.168 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0796 time to fit residues: 6.1532 Evaluate side-chains 58 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 32 optimal weight: 0.0060 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.191788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.171558 restraints weight = 5872.981| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.68 r_work: 0.3786 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 4790 Z= 0.110 Angle : 0.542 5.618 6553 Z= 0.276 Chirality : 0.040 0.163 737 Planarity : 0.004 0.040 793 Dihedral : 3.787 13.519 646 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.07 % Allowed : 8.90 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.36), residues: 584 helix: 1.87 (0.32), residues: 277 sheet: 0.16 (0.64), residues: 77 loop : -3.16 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.008 0.001 TYR H 112 PHE 0.007 0.001 PHE H 68 TRP 0.011 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4788) covalent geometry : angle 0.54036 ( 6549) SS BOND : bond 0.00700 ( 2) SS BOND : angle 1.69572 ( 4) hydrogen bonds : bond 0.03685 ( 222) hydrogen bonds : angle 3.97237 ( 630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.159 Fit side-chains REVERT: A 384 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6764 (mp) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.0706 time to fit residues: 5.4819 Evaluate side-chains 59 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.187859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168188 restraints weight = 5864.963| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.62 r_work: 0.3755 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4790 Z= 0.128 Angle : 0.569 6.639 6553 Z= 0.291 Chirality : 0.041 0.162 737 Planarity : 0.004 0.041 793 Dihedral : 3.955 16.770 646 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.66 % Allowed : 10.97 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.36), residues: 584 helix: 1.73 (0.32), residues: 277 sheet: -0.36 (0.57), residues: 94 loop : -3.25 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.012 0.001 TYR H 112 PHE 0.008 0.001 PHE H 68 TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4788) covalent geometry : angle 0.56784 ( 6549) SS BOND : bond 0.00699 ( 2) SS BOND : angle 1.64837 ( 4) hydrogen bonds : bond 0.04368 ( 222) hydrogen bonds : angle 4.03548 ( 630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.222 Fit side-chains REVERT: A 384 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6862 (mp) REVERT: H 111 MET cc_start: 0.9098 (ptm) cc_final: 0.8842 (ttp) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.0726 time to fit residues: 6.0092 Evaluate side-chains 66 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.190334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.170576 restraints weight = 5913.784| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.66 r_work: 0.3788 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 4790 Z= 0.109 Angle : 0.540 5.786 6553 Z= 0.276 Chirality : 0.040 0.162 737 Planarity : 0.004 0.040 793 Dihedral : 3.795 15.480 646 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.07 % Allowed : 10.97 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.36), residues: 584 helix: 1.82 (0.32), residues: 277 sheet: -0.47 (0.59), residues: 87 loop : -3.09 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.009 0.001 TYR H 112 PHE 0.007 0.001 PHE H 68 TRP 0.011 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4788) covalent geometry : angle 0.53892 ( 6549) SS BOND : bond 0.00597 ( 2) SS BOND : angle 1.33561 ( 4) hydrogen bonds : bond 0.03626 ( 222) hydrogen bonds : angle 3.90183 ( 630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.176 Fit side-chains REVERT: A 384 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6796 (mp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0806 time to fit residues: 6.3836 Evaluate side-chains 64 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.186297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.166739 restraints weight = 5869.081| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.62 r_work: 0.3741 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4790 Z= 0.137 Angle : 0.579 6.977 6553 Z= 0.296 Chirality : 0.042 0.167 737 Planarity : 0.004 0.041 793 Dihedral : 4.003 14.761 646 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.07 % Allowed : 12.22 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.35), residues: 584 helix: 1.64 (0.32), residues: 277 sheet: -0.38 (0.58), residues: 91 loop : -3.31 (0.33), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.011 0.001 TYR H 95 PHE 0.008 0.001 PHE H 68 TRP 0.013 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4788) covalent geometry : angle 0.57774 ( 6549) SS BOND : bond 0.00804 ( 2) SS BOND : angle 1.76393 ( 4) hydrogen bonds : bond 0.04648 ( 222) hydrogen bonds : angle 4.06330 ( 630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.148 Fit side-chains REVERT: A 384 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6905 (mp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0729 time to fit residues: 5.8870 Evaluate side-chains 63 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.188587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.168877 restraints weight = 5931.779| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.65 r_work: 0.3763 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4790 Z= 0.115 Angle : 0.558 5.896 6553 Z= 0.286 Chirality : 0.041 0.197 737 Planarity : 0.004 0.042 793 Dihedral : 3.880 15.146 646 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.28 % Allowed : 12.22 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.35), residues: 584 helix: 1.72 (0.32), residues: 277 sheet: -0.26 (0.59), residues: 89 loop : -3.24 (0.33), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.010 0.001 TYR H 112 PHE 0.006 0.001 PHE H 68 TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4788) covalent geometry : angle 0.55717 ( 6549) SS BOND : bond 0.00631 ( 2) SS BOND : angle 1.39619 ( 4) hydrogen bonds : bond 0.03904 ( 222) hydrogen bonds : angle 4.02666 ( 630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.159 Fit side-chains REVERT: A 384 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6845 (mp) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.0771 time to fit residues: 6.4477 Evaluate side-chains 66 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.186851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167685 restraints weight = 5813.819| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.61 r_work: 0.3745 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4790 Z= 0.138 Angle : 0.591 6.926 6553 Z= 0.303 Chirality : 0.043 0.219 737 Planarity : 0.004 0.040 793 Dihedral : 4.049 14.683 646 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.07 % Allowed : 12.63 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.35), residues: 584 helix: 1.56 (0.32), residues: 277 sheet: -0.27 (0.58), residues: 91 loop : -3.32 (0.33), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.012 0.001 TYR H 112 PHE 0.008 0.001 PHE H 68 TRP 0.014 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4788) covalent geometry : angle 0.58971 ( 6549) SS BOND : bond 0.00821 ( 2) SS BOND : angle 1.80021 ( 4) hydrogen bonds : bond 0.04722 ( 222) hydrogen bonds : angle 4.16278 ( 630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.157 Fit side-chains REVERT: A 384 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6900 (mp) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.0745 time to fit residues: 5.5744 Evaluate side-chains 62 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.186321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.166881 restraints weight = 5906.717| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.63 r_work: 0.3739 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4790 Z= 0.136 Angle : 0.592 6.786 6553 Z= 0.303 Chirality : 0.043 0.218 737 Planarity : 0.004 0.042 793 Dihedral : 4.082 13.532 646 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.07 % Allowed : 12.42 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.35), residues: 584 helix: 1.51 (0.32), residues: 277 sheet: -0.24 (0.58), residues: 91 loop : -3.34 (0.33), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.014 0.001 TYR A 75 PHE 0.007 0.001 PHE H 68 TRP 0.015 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4788) covalent geometry : angle 0.59103 ( 6549) SS BOND : bond 0.00738 ( 2) SS BOND : angle 1.75233 ( 4) hydrogen bonds : bond 0.04687 ( 222) hydrogen bonds : angle 4.18691 ( 630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.172 Fit side-chains REVERT: A 384 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6898 (mp) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.0761 time to fit residues: 6.0986 Evaluate side-chains 67 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.189495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.170059 restraints weight = 5808.901| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.69 r_work: 0.3793 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 4790 Z= 0.111 Angle : 0.556 5.853 6553 Z= 0.283 Chirality : 0.041 0.235 737 Planarity : 0.004 0.041 793 Dihedral : 3.847 13.807 646 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.86 % Allowed : 12.63 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.36), residues: 584 helix: 1.70 (0.32), residues: 277 sheet: -0.09 (0.60), residues: 89 loop : -3.22 (0.34), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.009 0.001 TYR H 112 PHE 0.006 0.001 PHE H 68 TRP 0.012 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4788) covalent geometry : angle 0.55545 ( 6549) SS BOND : bond 0.00638 ( 2) SS BOND : angle 1.27198 ( 4) hydrogen bonds : bond 0.03699 ( 222) hydrogen bonds : angle 4.00729 ( 630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.09 seconds wall clock time: 26 minutes 28.70 seconds (1588.70 seconds total)