Starting phenix.real_space_refine on Thu Jul 24 02:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dm7_46999/07_2025/9dm7_46999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dm7_46999/07_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_46999/07_2025/9dm7_46999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dm7_46999/07_2025/9dm7_46999.map" model { file = "/net/cci-nas-00/data/ceres_data/9dm7_46999/07_2025/9dm7_46999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dm7_46999/07_2025/9dm7_46999.cif" } resolution = 3.02 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= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.78, per 1000 atoms: 0.81 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: 0.98 Conformation dependent library (CDL) restraints added in 499.5 milliseconds 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: 0.46 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: 1.16 Time building geometry restraints manager: 1.20 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- 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 (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: -0.87 (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 TRP 0.038 0.001 TRP A 34 HIS 0.002 0.001 HIS A 321 PHE 0.013 0.001 PHE H 68 TYR 0.008 0.001 TYR A 75 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.17084 ( 222) hydrogen bonds : angle 6.41161 ( 630) SS BOND : bond 0.00430 ( 2) SS BOND : angle 1.13092 ( 4) covalent geometry : bond 0.00302 ( 4788) covalent geometry : angle 0.67354 ( 6549) *********************** 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 : 0.482 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: 0.1902 time to fit residues: 15.1198 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 : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.188082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.167979 restraints weight = 5758.034| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.64 r_work: 0.3737 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4790 Z= 0.154 Angle : 0.634 7.472 6553 Z= 0.323 Chirality : 0.043 0.170 737 Planarity : 0.005 0.044 793 Dihedral : 4.193 18.830 646 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.66 % Allowed : 6.00 % Favored : 92.34 % 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 (0.35), residues: 584 helix: 1.45 (0.32), residues: 277 sheet: -0.56 (0.56), residues: 98 loop : -3.40 (0.34), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 PHE 0.007 0.001 PHE H 68 TYR 0.013 0.002 TYR H 112 ARG 0.004 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 222) hydrogen bonds : angle 4.60724 ( 630) SS BOND : bond 0.00967 ( 2) SS BOND : angle 2.30071 ( 4) covalent geometry : bond 0.00347 ( 4788) covalent geometry : angle 0.63180 ( 6549) *********************** 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 63 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.386 Fit side-chains REVERT: A 209 ARG cc_start: 0.7056 (tpp-160) cc_final: 0.6775 (tpp80) REVERT: A 384 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6890 (mp) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1825 time to fit residues: 14.0325 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 : 0.440 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.186016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.166376 restraints weight = 5783.094| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.61 r_work: 0.3733 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4790 Z= 0.147 Angle : 0.609 7.238 6553 Z= 0.312 Chirality : 0.042 0.168 737 Planarity : 0.005 0.044 793 Dihedral : 4.255 17.562 646 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.66 % Allowed : 9.52 % Favored : 88.82 % 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: -0.69 (0.35), residues: 584 helix: 1.50 (0.32), residues: 277 sheet: -0.06 (0.60), residues: 85 loop : -3.36 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 377 HIS 0.004 0.001 HIS A 104 PHE 0.011 0.001 PHE H 68 TYR 0.012 0.001 TYR H 112 ARG 0.004 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 222) hydrogen bonds : angle 4.37768 ( 630) SS BOND : bond 0.00832 ( 2) SS BOND : angle 1.85503 ( 4) covalent geometry : bond 0.00335 ( 4788) covalent geometry : angle 0.60781 ( 6549) *********************** 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 65 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.454 Fit side-chains REVERT: A 384 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6917 (mp) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.2025 time to fit residues: 15.7381 Evaluate side-chains 60 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.189441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.169841 restraints weight = 5809.516| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.65 r_work: 0.3764 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1478 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= 0.117 Angle : 0.563 5.980 6553 Z= 0.288 Chirality : 0.041 0.174 737 Planarity : 0.004 0.043 793 Dihedral : 4.007 16.078 646 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.86 % Allowed : 10.35 % Favored : 87.78 % 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: -0.57 (0.36), residues: 584 helix: 1.67 (0.32), residues: 277 sheet: -0.39 (0.61), residues: 85 loop : -3.22 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 PHE 0.008 0.001 PHE H 68 TYR 0.009 0.001 TYR H 112 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 222) hydrogen bonds : angle 4.14002 ( 630) SS BOND : bond 0.00716 ( 2) SS BOND : angle 1.58685 ( 4) covalent geometry : bond 0.00263 ( 4788) covalent geometry : angle 0.56153 ( 6549) *********************** 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 67 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.426 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1720 time to fit residues: 13.8028 Evaluate side-chains 61 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.187267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167565 restraints weight = 5863.686| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.65 r_work: 0.3743 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1657 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= 0.130 Angle : 0.578 6.601 6553 Z= 0.297 Chirality : 0.041 0.164 737 Planarity : 0.004 0.042 793 Dihedral : 4.056 15.612 646 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.07 % Allowed : 11.80 % Favored : 86.13 % 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: -0.60 (0.35), residues: 584 helix: 1.63 (0.32), residues: 277 sheet: -0.23 (0.61), residues: 86 loop : -3.31 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.005 0.001 HIS A 52 PHE 0.007 0.001 PHE H 68 TYR 0.010 0.001 TYR H 112 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 222) hydrogen bonds : angle 4.13558 ( 630) SS BOND : bond 0.00749 ( 2) SS BOND : angle 1.80889 ( 4) covalent geometry : bond 0.00291 ( 4788) covalent geometry : angle 0.57622 ( 6549) *********************** 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: 10 poor density : 57 time to evaluate : 0.444 Fit side-chains REVERT: A 384 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6912 (mp) REVERT: H 6 GLU cc_start: 0.8483 (mp0) cc_final: 0.8268 (mt-10) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1639 time to fit residues: 13.5220 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 : 0.521 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.187411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.168095 restraints weight = 5732.255| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.62 r_work: 0.3764 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1752 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= 0.130 Angle : 0.576 6.635 6553 Z= 0.295 Chirality : 0.041 0.169 737 Planarity : 0.004 0.043 793 Dihedral : 4.068 15.692 646 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.48 % Allowed : 11.80 % 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 (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: -0.63 (0.35), residues: 584 helix: 1.59 (0.32), residues: 277 sheet: -0.35 (0.58), residues: 91 loop : -3.32 (0.33), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS A 104 PHE 0.008 0.001 PHE H 68 TYR 0.010 0.001 TYR H 112 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 222) hydrogen bonds : angle 4.13321 ( 630) SS BOND : bond 0.00716 ( 2) SS BOND : angle 1.63479 ( 4) covalent geometry : bond 0.00295 ( 4788) covalent geometry : angle 0.57466 ( 6549) *********************** 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 70 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.730 Fit side-chains REVERT: A 384 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6920 (mp) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.3462 time to fit residues: 30.1267 Evaluate side-chains 65 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.0060 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.190656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.170576 restraints weight = 5835.276| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.75 r_work: 0.3795 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1807 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= 0.107 Angle : 0.546 5.825 6553 Z= 0.280 Chirality : 0.040 0.165 737 Planarity : 0.004 0.041 793 Dihedral : 3.806 15.804 646 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.36), residues: 584 helix: 1.78 (0.32), residues: 277 sheet: -0.23 (0.62), residues: 82 loop : -3.10 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 PHE 0.006 0.001 PHE H 68 TYR 0.008 0.001 TYR H 95 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 222) hydrogen bonds : angle 3.95815 ( 630) SS BOND : bond 0.00553 ( 2) SS BOND : angle 1.26833 ( 4) covalent geometry : bond 0.00237 ( 4788) covalent geometry : angle 0.54479 ( 6549) *********************** 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 69 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.553 Fit side-chains REVERT: A 384 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6732 (mp) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.3123 time to fit residues: 26.9072 Evaluate side-chains 62 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 229 ILE Chi-restraints excluded: chain A residue 280 LEU 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 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0020 chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.2486 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.192479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.172803 restraints weight = 5784.211| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.73 r_work: 0.3801 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1869 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= 0.103 Angle : 0.539 5.599 6553 Z= 0.274 Chirality : 0.041 0.182 737 Planarity : 0.004 0.040 793 Dihedral : 3.674 14.936 646 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.69 % Allowed : 12.42 % Favored : 84.89 % 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: -0.29 (0.36), residues: 584 helix: 1.83 (0.32), residues: 277 sheet: -0.11 (0.62), residues: 82 loop : -3.01 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 PHE 0.006 0.001 PHE H 68 TYR 0.007 0.001 TYR H 112 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 222) hydrogen bonds : angle 3.84473 ( 630) SS BOND : bond 0.00568 ( 2) SS BOND : angle 1.21839 ( 4) covalent geometry : bond 0.00227 ( 4788) covalent geometry : angle 0.53798 ( 6549) *********************** 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 69 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.521 Fit side-chains REVERT: A 280 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6361 (mm) REVERT: A 303 GLN cc_start: 0.7846 (mt0) cc_final: 0.7589 (mt0) REVERT: A 384 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6700 (mp) REVERT: L 45 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7748 (mtmm) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.3124 time to fit residues: 26.3804 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 : 0.533 ------------------------------------------------------------------------------- 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 74 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 384 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 54 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 35 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 overall best weight: 0.5362 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.187998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168456 restraints weight = 5815.209| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.68 r_work: 0.3775 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1904 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= 0.121 Angle : 0.566 6.587 6553 Z= 0.289 Chirality : 0.042 0.209 737 Planarity : 0.004 0.041 793 Dihedral : 3.826 14.866 646 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.69 % Allowed : 12.42 % Favored : 84.89 % 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: -0.41 (0.36), residues: 584 helix: 1.70 (0.32), residues: 277 sheet: -0.04 (0.59), residues: 89 loop : -3.17 (0.34), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 PHE 0.007 0.001 PHE H 68 TYR 0.010 0.001 TYR H 95 ARG 0.001 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 222) hydrogen bonds : angle 3.97413 ( 630) SS BOND : bond 0.00719 ( 2) SS BOND : angle 1.60029 ( 4) covalent geometry : bond 0.00273 ( 4788) covalent geometry : angle 0.56523 ( 6549) *********************** 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 69 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.615 Fit side-chains REVERT: A 303 GLN cc_start: 0.7901 (mt0) cc_final: 0.7643 (mt0) REVERT: A 384 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6843 (mp) REVERT: L 45 LYS cc_start: 0.8143 (ptpp) cc_final: 0.7888 (mtmm) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.3701 time to fit residues: 34.4193 Evaluate side-chains 65 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 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 384 LEU Chi-restraints excluded: chain H residue 17 SER 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 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0050 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.187971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.168736 restraints weight = 5745.795| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.58 r_work: 0.3760 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1966 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= 0.125 Angle : 0.580 6.600 6553 Z= 0.294 Chirality : 0.043 0.267 737 Planarity : 0.004 0.041 793 Dihedral : 3.934 15.105 646 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % Favored : 84.89 % 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: -0.49 (0.35), residues: 584 helix: 1.63 (0.32), residues: 277 sheet: 0.02 (0.61), residues: 84 loop : -3.19 (0.34), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 377 HIS 0.003 0.001 HIS A 321 PHE 0.007 0.001 PHE H 68 TYR 0.016 0.001 TYR H 112 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 222) hydrogen bonds : angle 4.02666 ( 630) SS BOND : bond 0.00691 ( 2) SS BOND : angle 1.58069 ( 4) covalent geometry : bond 0.00283 ( 4788) covalent geometry : angle 0.57846 ( 6549) ********************** 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 66 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.582 Fit side-chains REVERT: A 384 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6862 (mp) REVERT: L 3 GLN cc_start: 0.7583 (mp10) cc_final: 0.7199 (mp10) REVERT: L 45 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7887 (mtmm) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.1622 time to fit residues: 12.9433 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 74 LEU 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 384 LEU Chi-restraints excluded: chain H residue 17 SER 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 11 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.187388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167990 restraints weight = 5809.893| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.59 r_work: 0.3753 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2026 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 : 0.585 6.549 6553 Z= 0.297 Chirality : 0.043 0.263 737 Planarity : 0.004 0.041 793 Dihedral : 3.980 15.783 646 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.28 % Allowed : 13.46 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.35), residues: 584 helix: 1.59 (0.32), residues: 277 sheet: 0.04 (0.61), residues: 84 loop : -3.20 (0.33), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 377 HIS 0.003 0.001 HIS A 104 PHE 0.007 0.001 PHE H 68 TYR 0.012 0.001 TYR H 112 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 222) hydrogen bonds : angle 4.06252 ( 630) SS BOND : bond 0.00747 ( 2) SS BOND : angle 1.67762 ( 4) covalent geometry : bond 0.00289 ( 4788) covalent geometry : angle 0.58331 ( 6549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4190.40 seconds wall clock time: 79 minutes 28.44 seconds (4768.44 seconds total)