Starting phenix.real_space_refine on Thu Jul 2 01:12:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8epa_28523/07_2026/8epa_28523.cif" } resolution = 3.4 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3179 2.51 5 N 872 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5045 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1580 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 173} Chain breaks: 1 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 918 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 897 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.34, per 1000 atoms: 0.27 Number of scatterers: 5045 At special positions: 0 Unit cell: (73.1, 63.64, 128.14, 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 24 16.00 O 970 8.00 N 872 7.00 C 3179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 160 " - pdb=" SG CYS I 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN I 49 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 184.2 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 16 sheets defined 2.5% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.567A pdb=" N PHE A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.103A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.799A pdb=" N GLN I 39 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 78 through 79 removed outlier: 3.752A pdb=" N TYR I 67 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN I 109 " --> pdb=" O HIS I 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE I 106 " --> pdb=" O LEU I 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 141 removed outlier: 5.613A pdb=" N ASN I 137 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN I 153 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 176 through 180 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.945A pdb=" N THR H 69 " --> pdb=" O HIS H 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU H 33 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.718A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.659A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.673A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.872A pdb=" N VAL A 12 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.872A pdb=" N VAL A 12 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.533A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 339 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: 0.55 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: 1.23 - 1.34: 1627 1.34 - 1.46: 1328 1.46 - 1.58: 2184 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5173 Sorted by residual: bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CG1 ILE H 70 " pdb=" CD1 ILE H 70 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 bond pdb=" CB PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.03e+00 ... (remaining 5168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 6919 2.46 - 4.91: 93 4.91 - 7.37: 4 7.37 - 9.82: 1 9.82 - 12.28: 1 Bond angle restraints: 7018 Sorted by residual: angle pdb=" CB LYS L 45 " pdb=" CG LYS L 45 " pdb=" CD LYS L 45 " ideal model delta sigma weight residual 111.30 118.72 -7.42 2.30e+00 1.89e-01 1.04e+01 angle pdb=" N SER L 52 " pdb=" CA SER L 52 " pdb=" C SER L 52 " ideal model delta sigma weight residual 114.62 111.13 3.49 1.14e+00 7.69e-01 9.38e+00 angle pdb=" C ILE H 48 " pdb=" N SER H 49 " pdb=" CA SER H 49 " ideal model delta sigma weight residual 121.75 116.65 5.10 1.73e+00 3.34e-01 8.70e+00 angle pdb=" C ASP H 109 " pdb=" N ILE H 110 " pdb=" CA ILE H 110 " ideal model delta sigma weight residual 121.97 127.21 -5.24 1.80e+00 3.09e-01 8.47e+00 angle pdb=" CA SER L 52 " pdb=" C SER L 52 " pdb=" N ASN L 53 " ideal model delta sigma weight residual 119.71 116.73 2.98 1.17e+00 7.31e-01 6.47e+00 ... (remaining 7013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 2684 16.38 - 32.76: 276 32.76 - 49.14: 57 49.14 - 65.51: 8 65.51 - 81.89: 8 Dihedral angle restraints: 3033 sinusoidal: 1198 harmonic: 1835 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA HIS I 141 " pdb=" C HIS I 141 " pdb=" N LYS I 142 " pdb=" CA LYS I 142 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS I 160 " pdb=" SG CYS I 160 " pdb=" SG CYS I 209 " pdb=" CB CYS I 209 " ideal model delta sinusoidal sigma weight residual -86.00 -53.76 -32.24 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 3030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 570 0.047 - 0.093: 136 0.093 - 0.140: 47 0.140 - 0.186: 3 0.186 - 0.233: 1 Chirality restraints: 757 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN I 49 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ASN I 137 " pdb=" N ASN I 137 " pdb=" C ASN I 137 " pdb=" CB ASN I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 754 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO L 8 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 206 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO I 207 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 360 2.73 - 3.27: 5009 3.27 - 3.81: 8017 3.81 - 4.36: 9185 4.36 - 4.90: 16263 Nonbonded interactions: 38834 Sorted by model distance: nonbonded pdb=" OG1 THR L 20 " pdb=" OG1 THR L 72 " model vdw 2.184 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.189 3.120 nonbonded pdb=" OE2 GLU A 6 " pdb=" OG1 THR A 116 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.238 3.040 nonbonded pdb=" OG SER H 52 " pdb=" OG1 THR H 56 " model vdw 2.240 3.040 ... (remaining 38829 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.004 0.051 5182 Z= 0.172 Angle : 0.698 12.281 7038 Z= 0.360 Chirality : 0.046 0.233 757 Planarity : 0.005 0.075 896 Dihedral : 14.000 81.892 1838 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.28 % Favored : 90.40 % Rotamer: Outliers : 0.18 % Allowed : 1.08 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.16 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.53 (0.35), residues: 228 loop : -2.10 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 196 TYR 0.018 0.001 TYR H 50 PHE 0.012 0.002 PHE A 29 TRP 0.010 0.001 TRP I 175 HIS 0.003 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 5173) covalent geometry : angle 0.69262 / 0.36 ( 7018) SS BOND : bond 0.00435 / 0.22 ( 7) SS BOND : angle 1.17423 / 0.58 ( 14) hydrogen bonds : bond 0.25297 / 16.58 ( 130) hydrogen bonds : angle 9.40427 / 6.67 ( 339) link_BETA1-4 : bond 0.00466 / 0.25 ( 1) link_BETA1-4 : angle 2.90765 / 1.38 ( 3) link_NAG-ASN : bond 0.00604 / 0.32 ( 1) link_NAG-ASN : angle 2.47397 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: I 39 GLN cc_start: 0.7978 (mp10) cc_final: 0.7687 (mp10) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0777 time to fit residues: 8.4878 Evaluate side-chains 74 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.093997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082936 restraints weight = 15374.348| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.78 r_work: 0.3421 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5182 Z= 0.226 Angle : 0.746 12.218 7038 Z= 0.383 Chirality : 0.049 0.155 757 Planarity : 0.005 0.054 896 Dihedral : 5.361 20.969 693 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.60 % Favored : 90.08 % Rotamer: Outliers : 0.72 % Allowed : 10.93 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.24 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.93 (0.33), residues: 250 loop : -1.93 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 196 TYR 0.011 0.002 TYR A 60 PHE 0.015 0.002 PHE I 106 TRP 0.013 0.001 TRP I 52 HIS 0.006 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 ( 5173) covalent geometry : angle 0.74251 / 0.38 ( 7018) SS BOND : bond 0.00534 / 0.27 ( 7) SS BOND : angle 0.91872 / 0.48 ( 14) hydrogen bonds : bond 0.04983 / 3.25 ( 130) hydrogen bonds : angle 7.43872 / 5.31 ( 339) link_BETA1-4 : bond 0.00229 / 0.12 ( 1) link_BETA1-4 : angle 2.33079 / 1.14 ( 3) link_NAG-ASN : bond 0.00544 / 0.29 ( 1) link_NAG-ASN : angle 2.70200 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.0744 time to fit residues: 8.3691 Evaluate side-chains 79 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.096440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085271 restraints weight = 15545.653| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.89 r_work: 0.3464 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5182 Z= 0.137 Angle : 0.665 10.969 7038 Z= 0.338 Chirality : 0.047 0.180 757 Planarity : 0.005 0.049 896 Dihedral : 5.025 17.147 693 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 1.25 % Allowed : 14.34 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.06 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.55 (0.35), residues: 229 loop : -1.97 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.013 0.001 TYR I 182 PHE 0.011 0.001 PHE I 106 TRP 0.013 0.001 TRP I 52 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 5173) covalent geometry : angle 0.66133 / 0.34 ( 7018) SS BOND : bond 0.00423 / 0.23 ( 7) SS BOND : angle 0.91897 / 0.46 ( 14) hydrogen bonds : bond 0.03931 / 2.55 ( 130) hydrogen bonds : angle 6.85353 / 4.89 ( 339) link_BETA1-4 : bond 0.00246 / 0.13 ( 1) link_BETA1-4 : angle 2.14737 / 1.03 ( 3) link_NAG-ASN : bond 0.00785 / 0.41 ( 1) link_NAG-ASN : angle 2.68399 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 142 LYS cc_start: 0.7963 (tttm) cc_final: 0.7623 (tptt) REVERT: L 66 ARG cc_start: 0.9133 (tmm-80) cc_final: 0.8906 (tmm-80) REVERT: A 34 MET cc_start: 0.8644 (mmm) cc_final: 0.8395 (mmm) REVERT: A 38 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8165 (ttp80) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.0739 time to fit residues: 8.9278 Evaluate side-chains 86 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.097207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085904 restraints weight = 15526.061| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.92 r_work: 0.3478 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5182 Z= 0.125 Angle : 0.657 10.824 7038 Z= 0.330 Chirality : 0.046 0.180 757 Planarity : 0.005 0.048 896 Dihedral : 4.842 17.105 693 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.64 % Favored : 91.04 % Rotamer: Outliers : 1.61 % Allowed : 17.56 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -1.98 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.42 (0.35), residues: 229 loop : -1.97 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.015 0.001 TYR I 182 PHE 0.010 0.001 PHE I 106 TRP 0.012 0.001 TRP I 52 HIS 0.004 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5173) covalent geometry : angle 0.65265 / 0.33 ( 7018) SS BOND : bond 0.00402 / 0.22 ( 7) SS BOND : angle 0.87847 / 0.44 ( 14) hydrogen bonds : bond 0.03556 / 2.36 ( 130) hydrogen bonds : angle 6.50805 / 4.67 ( 339) link_BETA1-4 : bond 0.00401 / 0.21 ( 1) link_BETA1-4 : angle 2.19798 / 1.05 ( 3) link_NAG-ASN : bond 0.00728 / 0.38 ( 1) link_NAG-ASN : angle 2.71116 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8584 (t0) cc_final: 0.8321 (t0) REVERT: I 142 LYS cc_start: 0.7880 (tttm) cc_final: 0.7557 (tptt) REVERT: L 66 ARG cc_start: 0.9150 (tmm-80) cc_final: 0.8922 (tmm-80) REVERT: A 38 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8234 (ttp80) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.0613 time to fit residues: 7.0242 Evaluate side-chains 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.098219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086820 restraints weight = 15870.302| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.00 r_work: 0.3494 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5182 Z= 0.111 Angle : 0.641 10.849 7038 Z= 0.320 Chirality : 0.045 0.184 757 Planarity : 0.004 0.048 896 Dihedral : 4.663 17.290 693 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 1.61 % Allowed : 19.18 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -1.94 (0.32), residues: 625 helix: None (None), residues: 0 sheet: -0.39 (0.35), residues: 228 loop : -1.94 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.015 0.001 TYR I 182 PHE 0.009 0.001 PHE I 106 TRP 0.011 0.001 TRP I 52 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5173) covalent geometry : angle 0.63679 / 0.32 ( 7018) SS BOND : bond 0.00353 / 0.19 ( 7) SS BOND : angle 0.79924 / 0.40 ( 14) hydrogen bonds : bond 0.03248 / 2.17 ( 130) hydrogen bonds : angle 6.25575 / 4.50 ( 339) link_BETA1-4 : bond 0.00466 / 0.25 ( 1) link_BETA1-4 : angle 2.16642 / 1.03 ( 3) link_NAG-ASN : bond 0.00725 / 0.38 ( 1) link_NAG-ASN : angle 2.68821 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8572 (t0) cc_final: 0.8272 (t0) REVERT: I 118 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6859 (mtp180) REVERT: I 142 LYS cc_start: 0.7849 (tttm) cc_final: 0.7438 (tttp) REVERT: L 66 ARG cc_start: 0.9152 (tmm-80) cc_final: 0.8930 (tmm-80) REVERT: A 34 MET cc_start: 0.8590 (mmm) cc_final: 0.8307 (mmm) REVERT: B 38 GLN cc_start: 0.7840 (tp40) cc_final: 0.7429 (tp40) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.0803 time to fit residues: 10.0218 Evaluate side-chains 91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN L 37 GLN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.093490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082073 restraints weight = 16125.715| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.93 r_work: 0.3388 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5182 Z= 0.238 Angle : 0.764 12.965 7038 Z= 0.388 Chirality : 0.048 0.189 757 Planarity : 0.005 0.050 896 Dihedral : 5.249 19.263 693 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.36 % Favored : 88.32 % Rotamer: Outliers : 2.15 % Allowed : 19.35 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.18 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.77 (0.33), residues: 259 loop : -2.01 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 61 TYR 0.012 0.002 TYR I 182 PHE 0.011 0.002 PHE L 49 TRP 0.014 0.002 TRP I 52 HIS 0.006 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 ( 5173) covalent geometry : angle 0.75989 / 0.39 ( 7018) SS BOND : bond 0.00583 / 0.28 ( 7) SS BOND : angle 0.99694 / 0.50 ( 14) hydrogen bonds : bond 0.04473 / 2.95 ( 130) hydrogen bonds : angle 6.73865 / 4.83 ( 339) link_BETA1-4 : bond 0.00259 / 0.14 ( 1) link_BETA1-4 : angle 2.45981 / 1.18 ( 3) link_NAG-ASN : bond 0.00589 / 0.31 ( 1) link_NAG-ASN : angle 2.67525 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8628 (t0) cc_final: 0.8351 (t0) REVERT: I 118 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6938 (mtp180) REVERT: I 142 LYS cc_start: 0.7956 (tttm) cc_final: 0.7695 (tptt) REVERT: H 76 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8196 (tptp) REVERT: L 45 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7941 (mmmm) REVERT: A 34 MET cc_start: 0.8787 (mmm) cc_final: 0.8416 (mmm) REVERT: B 38 GLN cc_start: 0.7845 (tp40) cc_final: 0.7360 (tp40) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.0749 time to fit residues: 8.5125 Evaluate side-chains 87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.096321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084873 restraints weight = 15714.810| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.94 r_work: 0.3459 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5182 Z= 0.129 Angle : 0.689 11.417 7038 Z= 0.343 Chirality : 0.046 0.182 757 Planarity : 0.004 0.052 896 Dihedral : 4.926 17.851 693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.16 % Favored : 91.52 % Rotamer: Outliers : 1.79 % Allowed : 21.68 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.02 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.59 (0.34), residues: 241 loop : -1.92 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.014 0.001 TYR I 182 PHE 0.009 0.001 PHE I 106 TRP 0.012 0.001 TRP B 35 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5173) covalent geometry : angle 0.68554 / 0.34 ( 7018) SS BOND : bond 0.00385 / 0.21 ( 7) SS BOND : angle 0.85555 / 0.43 ( 14) hydrogen bonds : bond 0.03426 / 2.28 ( 130) hydrogen bonds : angle 6.39899 / 4.60 ( 339) link_BETA1-4 : bond 0.00396 / 0.21 ( 1) link_BETA1-4 : angle 2.30669 / 1.10 ( 3) link_NAG-ASN : bond 0.00755 / 0.40 ( 1) link_NAG-ASN : angle 2.64723 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8586 (t0) cc_final: 0.8286 (t0) REVERT: I 118 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6813 (mtp180) REVERT: I 142 LYS cc_start: 0.7915 (tttm) cc_final: 0.7486 (tttp) REVERT: H 76 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8163 (tptp) REVERT: L 3 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8124 (tm-30) REVERT: L 45 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7966 (mmmm) outliers start: 10 outliers final: 9 residues processed: 97 average time/residue: 0.0738 time to fit residues: 9.0029 Evaluate side-chains 88 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.094816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.083623 restraints weight = 15463.785| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.83 r_work: 0.3431 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5182 Z= 0.167 Angle : 0.733 12.126 7038 Z= 0.367 Chirality : 0.048 0.287 757 Planarity : 0.004 0.048 896 Dihedral : 5.096 18.606 693 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.24 % Favored : 89.44 % Rotamer: Outliers : 2.69 % Allowed : 21.15 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.06 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.62 (0.34), residues: 242 loop : -1.96 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.013 0.001 TYR B 86 PHE 0.008 0.001 PHE I 106 TRP 0.013 0.002 TRP I 52 HIS 0.005 0.001 HIS I 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 5173) covalent geometry : angle 0.72954 / 0.37 ( 7018) SS BOND : bond 0.00537 / 0.28 ( 7) SS BOND : angle 0.91439 / 0.46 ( 14) hydrogen bonds : bond 0.03818 / 2.56 ( 130) hydrogen bonds : angle 6.53383 / 4.66 ( 339) link_BETA1-4 : bond 0.00366 / 0.19 ( 1) link_BETA1-4 : angle 2.42986 / 1.17 ( 3) link_NAG-ASN : bond 0.00675 / 0.36 ( 1) link_NAG-ASN : angle 2.65745 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8604 (t0) cc_final: 0.8335 (t0) REVERT: I 118 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6822 (mtp180) REVERT: I 142 LYS cc_start: 0.7951 (tttm) cc_final: 0.7593 (tttp) REVERT: H 76 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8174 (tptp) REVERT: L 3 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8207 (tm-30) REVERT: L 45 LYS cc_start: 0.8173 (mmmm) cc_final: 0.7971 (mmmm) REVERT: A 34 MET cc_start: 0.8622 (mmm) cc_final: 0.8342 (mmm) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.0738 time to fit residues: 8.7867 Evaluate side-chains 92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.097561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.086070 restraints weight = 15561.206| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.93 r_work: 0.3482 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5182 Z= 0.123 Angle : 0.709 9.418 7038 Z= 0.351 Chirality : 0.047 0.212 757 Planarity : 0.005 0.052 896 Dihedral : 4.908 18.670 693 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 2.33 % Allowed : 22.58 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -1.97 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.54 (0.34), residues: 241 loop : -1.90 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.015 0.001 TYR B 86 PHE 0.008 0.001 PHE I 106 TRP 0.012 0.001 TRP B 35 HIS 0.004 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5173) covalent geometry : angle 0.70490 / 0.35 ( 7018) SS BOND : bond 0.00413 / 0.22 ( 7) SS BOND : angle 0.89593 / 0.44 ( 14) hydrogen bonds : bond 0.03357 / 2.27 ( 130) hydrogen bonds : angle 6.38549 / 4.55 ( 339) link_BETA1-4 : bond 0.00474 / 0.25 ( 1) link_BETA1-4 : angle 2.28124 / 1.09 ( 3) link_NAG-ASN : bond 0.00740 / 0.39 ( 1) link_NAG-ASN : angle 2.62053 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8548 (t0) cc_final: 0.8253 (t0) REVERT: I 118 ARG cc_start: 0.7084 (mtp180) cc_final: 0.6818 (mtp180) REVERT: I 142 LYS cc_start: 0.7844 (tttm) cc_final: 0.7392 (tttp) REVERT: H 76 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8154 (tptp) REVERT: L 3 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 34 MET cc_start: 0.8570 (mmm) cc_final: 0.8285 (mmm) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.0741 time to fit residues: 9.1107 Evaluate side-chains 92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084937 restraints weight = 15862.281| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.03 r_work: 0.3452 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5182 Z= 0.140 Angle : 0.739 9.860 7038 Z= 0.369 Chirality : 0.048 0.213 757 Planarity : 0.004 0.048 896 Dihedral : 4.886 18.843 693 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.44 % Favored : 90.24 % Rotamer: Outliers : 2.33 % Allowed : 23.12 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -1.99 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.52 (0.35), residues: 230 loop : -1.91 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.013 0.001 TYR I 182 PHE 0.049 0.002 PHE A 68 TRP 0.012 0.001 TRP I 52 HIS 0.004 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5173) covalent geometry : angle 0.73552 / 0.37 ( 7018) SS BOND : bond 0.00473 / 0.25 ( 7) SS BOND : angle 0.83151 / 0.42 ( 14) hydrogen bonds : bond 0.03552 / 2.35 ( 130) hydrogen bonds : angle 6.48724 / 4.63 ( 339) link_BETA1-4 : bond 0.00484 / 0.25 ( 1) link_BETA1-4 : angle 2.33089 / 1.11 ( 3) link_NAG-ASN : bond 0.00697 / 0.37 ( 1) link_NAG-ASN : angle 2.62863 / 1.24 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: I 74 ASN cc_start: 0.8524 (t0) cc_final: 0.8250 (t0) REVERT: I 118 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6850 (mtp180) REVERT: I 142 LYS cc_start: 0.7834 (tttm) cc_final: 0.7370 (tttp) REVERT: H 76 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8168 (tptp) REVERT: L 3 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 34 MET cc_start: 0.8679 (mmm) cc_final: 0.8405 (mmm) REVERT: A 94 TYR cc_start: 0.5902 (m-10) cc_final: 0.5635 (m-10) outliers start: 13 outliers final: 12 residues processed: 88 average time/residue: 0.0699 time to fit residues: 8.0362 Evaluate side-chains 93 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 141 HIS Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.094336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.082862 restraints weight = 15710.578| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.93 r_work: 0.3418 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5182 Z= 0.175 Angle : 0.767 9.686 7038 Z= 0.385 Chirality : 0.049 0.252 757 Planarity : 0.005 0.049 896 Dihedral : 5.093 19.516 693 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.28 % Favored : 90.40 % Rotamer: Outliers : 2.69 % Allowed : 23.12 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 are not related in a simple way. whole: -2.16 (0.33), residues: 625 helix: None (None), residues: 0 sheet: -0.76 (0.33), residues: 248 loop : -1.97 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 61 TYR 0.012 0.001 TYR B 86 PHE 0.040 0.002 PHE A 68 TRP 0.013 0.001 TRP I 52 HIS 0.005 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 5173) covalent geometry : angle 0.76350 / 0.38 ( 7018) SS BOND : bond 0.00528 / 0.27 ( 7) SS BOND : angle 0.91116 / 0.46 ( 14) hydrogen bonds : bond 0.03952 / 2.60 ( 130) hydrogen bonds : angle 6.56279 / 4.67 ( 339) link_BETA1-4 : bond 0.00374 / 0.20 ( 1) link_BETA1-4 : angle 2.46835 / 1.19 ( 3) link_NAG-ASN : bond 0.00644 / 0.34 ( 1) link_NAG-ASN : angle 2.62344 / 1.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1120.47 seconds wall clock time: 20 minutes 1.26 seconds (1201.26 seconds total)