Starting phenix.real_space_refine on Tue Aug 4 13:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.map" model { file = "/net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uhq_64172/08_2026/9uhq_64172.cif" } resolution = 4.62 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= 0.036 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 16 5.16 5 C 2105 2.51 5 N 560 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3312 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1589 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 184} Chain: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 0.69, per 1000 atoms: 0.21 Number of scatterers: 3312 At special positions: 0 Unit cell: (62.06, 80.25, 98.44, 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 631 8.00 N 560 7.00 C 2105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 30 " distance=2.04 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 156 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.22 Conformation dependent library (CDL) restraints added in 81.2 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 16.3% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.669A pdb=" N GLU A 9 " --> pdb=" O PRO A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.896A pdb=" N VAL A 36 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 37 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 40 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 5.374A pdb=" N ASN A 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 removed outlier: 4.080A pdb=" N SER A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.779A pdb=" N ASN C 32 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.645A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 3.743A pdb=" N ASN A 23 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 68 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 64 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 63 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 102 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS A 47 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.567A pdb=" N TYR A 122 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 161 " --> pdb=" O TYR A 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.610A pdb=" N THR B 5 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.818A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.008A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 removed outlier: 4.026A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.551A pdb=" N THR C 113 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 249 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: 0.42 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1063 1.35 - 1.47: 917 1.47 - 1.59: 1399 1.59 - 1.72: 0 1.72 - 1.84: 20 Bond restraints: 3399 Sorted by residual: bond pdb=" CA GLU A 9 " pdb=" C GLU A 9 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.41e-02 5.03e+03 4.72e+00 bond pdb=" C HIS A 8 " pdb=" N GLU A 9 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.52e-02 4.33e+03 1.53e+00 bond pdb=" CA CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sigma weight residual 1.528 1.547 -0.018 1.49e-02 4.50e+03 1.48e+00 bond pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB ASP B 70 " pdb=" CG ASP B 70 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4439 1.89 - 3.78: 149 3.78 - 5.67: 23 5.67 - 7.56: 6 7.56 - 9.45: 1 Bond angle restraints: 4618 Sorted by residual: angle pdb=" C ASN B 30 " pdb=" CA ASN B 30 " pdb=" CB ASN B 30 " ideal model delta sigma weight residual 117.23 110.95 6.28 1.36e+00 5.41e-01 2.14e+01 angle pdb=" CA ASN B 30 " pdb=" C ASN B 30 " pdb=" N ASN B 31 " ideal model delta sigma weight residual 119.98 116.86 3.12 8.50e-01 1.38e+00 1.35e+01 angle pdb=" N SER A 35 " pdb=" CA SER A 35 " pdb=" C SER A 35 " ideal model delta sigma weight residual 113.01 108.78 4.23 1.20e+00 6.94e-01 1.25e+01 angle pdb=" CG ARG C 103 " pdb=" CD ARG C 103 " pdb=" NE ARG C 103 " ideal model delta sigma weight residual 112.00 119.14 -7.14 2.20e+00 2.07e-01 1.05e+01 angle pdb=" CB LEU C 85 " pdb=" CG LEU C 85 " pdb=" CD2 LEU C 85 " ideal model delta sigma weight residual 110.70 101.25 9.45 3.00e+00 1.11e-01 9.93e+00 ... (remaining 4613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 1823 15.96 - 31.92: 139 31.92 - 47.88: 32 47.88 - 63.84: 7 63.84 - 79.79: 5 Dihedral angle restraints: 2006 sinusoidal: 785 harmonic: 1221 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual -86.00 -7.05 -78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -37.62 -48.38 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual 93.00 48.01 44.99 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 2003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 330 0.043 - 0.086: 115 0.086 - 0.129: 42 0.129 - 0.172: 3 0.172 - 0.215: 1 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU C 85 " pdb=" CB LEU C 85 " pdb=" CD1 LEU C 85 " pdb=" CD2 LEU C 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 488 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 103 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ARG C 103 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG C 103 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA C 104 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 70 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASP B 70 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP B 70 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 43 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 44 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.021 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 1673 2.97 - 3.45: 3181 3.45 - 3.93: 5297 3.93 - 4.42: 5767 4.42 - 4.90: 9203 Nonbonded interactions: 25121 Sorted by model distance: nonbonded pdb=" N GLU B 81 " pdb=" OE1 GLU B 81 " model vdw 2.482 3.120 nonbonded pdb=" O ASP B 70 " pdb=" OD1 ASP B 70 " model vdw 2.486 3.040 nonbonded pdb=" OD1 ASP B 17 " pdb=" N ARG B 18 " model vdw 2.511 3.120 nonbonded pdb=" N GLN B 100 " pdb=" OE1 GLN B 100 " model vdw 2.513 3.120 nonbonded pdb=" OD1 ASN A 86 " pdb=" N ILE A 87 " model vdw 2.559 3.120 ... (remaining 25116 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 group one per residue 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.570 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:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 0.040 3405 Z= 0.211 Angle : 0.848 9.453 4630 Z= 0.473 Chirality : 0.048 0.215 491 Planarity : 0.005 0.050 601 Dihedral : 12.479 79.795 1214 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.49 (0.40), residues: 418 helix: -3.49 (0.72), residues: 20 sheet: 0.62 (0.48), residues: 115 loop : -0.48 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 18 TYR 0.015 0.002 TYR A 163 PHE 0.018 0.002 PHE B 71 TRP 0.015 0.002 TRP B 35 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 ( 3399) covalent geometry : angle 0.83713 / 0.47 ( 4618) SS BOND : bond 0.00857 / 0.45 ( 6) SS BOND : angle 2.82450 / 1.47 ( 12) hydrogen bonds : bond 0.30281 / 20.02 ( 108) hydrogen bonds : angle 10.21684 / 6.87 ( 249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LEU cc_start: 0.9060 (pt) cc_final: 0.8798 (pp) REVERT: A 72 LYS cc_start: 0.9266 (ptmm) cc_final: 0.8683 (ptmm) REVERT: A 78 GLN cc_start: 0.9355 (mp10) cc_final: 0.8857 (mp10) REVERT: A 86 ASN cc_start: 0.8879 (p0) cc_final: 0.8433 (p0) REVERT: A 169 TYR cc_start: 0.6463 (m-10) cc_final: 0.6198 (m-10) REVERT: B 33 LEU cc_start: 0.8844 (tp) cc_final: 0.8420 (tp) REVERT: B 34 ASN cc_start: 0.9039 (m-40) cc_final: 0.8476 (p0) REVERT: B 39 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8878 (mmtt) REVERT: B 46 LEU cc_start: 0.9010 (tp) cc_final: 0.8711 (tp) REVERT: B 58 VAL cc_start: 0.8309 (t) cc_final: 0.7983 (t) REVERT: B 62 PHE cc_start: 0.8780 (m-80) cc_final: 0.8294 (m-80) REVERT: B 103 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8775 (mtmm) REVERT: C 86 THR cc_start: 0.7889 (p) cc_final: 0.7316 (p) REVERT: C 89 ASP cc_start: 0.9094 (m-30) cc_final: 0.8784 (m-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0588 time to fit residues: 9.5033 Evaluate side-chains 116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0370 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3492 r_free = 0.3492 target = 0.102993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088028 restraints weight = 10512.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091171 restraints weight = 6102.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093359 restraints weight = 3988.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094868 restraints weight = 2818.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095973 restraints weight = 2120.848| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3405 Z= 0.127 Angle : 0.617 5.115 4630 Z= 0.328 Chirality : 0.046 0.155 491 Planarity : 0.004 0.033 601 Dihedral : 5.813 77.260 468 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.28 % Allowed : 3.32 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.49 (0.41), residues: 418 helix: -3.37 (0.68), residues: 32 sheet: 0.26 (0.44), residues: 137 loop : -0.15 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 18 TYR 0.012 0.001 TYR A 122 PHE 0.014 0.001 PHE B 71 TRP 0.016 0.002 TRP C 36 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 3399) covalent geometry : angle 0.61330 / 0.33 ( 4618) SS BOND : bond 0.00578 / 0.33 ( 6) SS BOND : angle 1.52963 / 0.77 ( 12) hydrogen bonds : bond 0.03993 / 2.61 ( 108) hydrogen bonds : angle 6.77323 / 4.42 ( 249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LEU cc_start: 0.8877 (pt) cc_final: 0.8634 (pp) REVERT: A 78 GLN cc_start: 0.9307 (mp10) cc_final: 0.8850 (mp10) REVERT: B 34 ASN cc_start: 0.9140 (m-40) cc_final: 0.8567 (p0) REVERT: B 35 TRP cc_start: 0.9065 (m100) cc_final: 0.8110 (m100) REVERT: B 46 LEU cc_start: 0.8924 (tp) cc_final: 0.8669 (tp) REVERT: B 50 ASP cc_start: 0.9368 (m-30) cc_final: 0.9109 (m-30) REVERT: C 33 TYR cc_start: 0.9073 (m-10) cc_final: 0.8814 (m-10) REVERT: C 39 GLN cc_start: 0.8923 (tt0) cc_final: 0.8717 (tp40) REVERT: C 45 LEU cc_start: 0.8527 (mp) cc_final: 0.7995 (mp) REVERT: C 51 ILE cc_start: 0.8859 (tt) cc_final: 0.8656 (tt) REVERT: C 76 ASN cc_start: 0.8540 (t0) cc_final: 0.8324 (t0) REVERT: C 86 THR cc_start: 0.7703 (p) cc_final: 0.6997 (p) REVERT: C 89 ASP cc_start: 0.8867 (m-30) cc_final: 0.8524 (m-30) REVERT: C 99 ILE cc_start: 0.9081 (mp) cc_final: 0.8590 (tp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.0477 time to fit residues: 7.4816 Evaluate side-chains 112 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3504 r_free = 0.3504 target = 0.103863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.088840 restraints weight = 11123.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092059 restraints weight = 6288.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094288 restraints weight = 4053.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095788 restraints weight = 2843.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096854 restraints weight = 2137.802| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3405 Z= 0.113 Angle : 0.596 5.723 4630 Z= 0.311 Chirality : 0.045 0.149 491 Planarity : 0.003 0.031 601 Dihedral : 5.792 79.693 468 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.41 (0.42), residues: 418 helix: -3.37 (0.67), residues: 32 sheet: 0.39 (0.43), residues: 142 loop : -0.15 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.007 0.001 TYR A 163 PHE 0.016 0.001 PHE B 71 TRP 0.012 0.002 TRP C 36 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 3399) covalent geometry : angle 0.59033 / 0.31 ( 4618) SS BOND : bond 0.00534 / 0.30 ( 6) SS BOND : angle 1.66873 / 0.83 ( 12) hydrogen bonds : bond 0.03647 / 2.31 ( 108) hydrogen bonds : angle 6.55438 / 4.30 ( 249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LEU cc_start: 0.8970 (pt) cc_final: 0.8742 (pp) REVERT: A 78 GLN cc_start: 0.9309 (mp10) cc_final: 0.8794 (mp10) REVERT: A 177 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7671 (mtt90) REVERT: B 34 ASN cc_start: 0.9134 (m-40) cc_final: 0.8681 (p0) REVERT: B 39 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8585 (mmtt) REVERT: B 50 ASP cc_start: 0.9423 (m-30) cc_final: 0.9209 (m-30) REVERT: C 32 ASN cc_start: 0.8787 (p0) cc_final: 0.8359 (p0) REVERT: C 33 TYR cc_start: 0.9016 (m-10) cc_final: 0.8706 (m-10) REVERT: C 34 MET cc_start: 0.8700 (mtm) cc_final: 0.8375 (mtt) REVERT: C 45 LEU cc_start: 0.8601 (mp) cc_final: 0.8091 (mp) REVERT: C 76 ASN cc_start: 0.8505 (t0) cc_final: 0.8274 (t0) REVERT: C 86 THR cc_start: 0.7622 (p) cc_final: 0.6961 (p) REVERT: C 89 ASP cc_start: 0.8898 (m-30) cc_final: 0.8504 (m-30) REVERT: C 94 TYR cc_start: 0.8371 (m-10) cc_final: 0.8154 (m-10) REVERT: C 98 ASP cc_start: 0.9480 (p0) cc_final: 0.9280 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0455 time to fit residues: 7.0350 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.100731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085673 restraints weight = 11473.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088884 restraints weight = 6558.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091092 restraints weight = 4262.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092640 restraints weight = 3008.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093751 restraints weight = 2242.702| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3405 Z= 0.141 Angle : 0.612 5.984 4630 Z= 0.325 Chirality : 0.046 0.142 491 Planarity : 0.004 0.032 601 Dihedral : 6.313 88.101 468 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.51 (0.42), residues: 418 helix: -3.48 (0.67), residues: 32 sheet: 0.37 (0.44), residues: 142 loop : -0.25 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 38 TYR 0.009 0.001 TYR C 59 PHE 0.011 0.001 PHE A 11 TRP 0.011 0.002 TRP C 36 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3399) covalent geometry : angle 0.60696 / 0.32 ( 4618) SS BOND : bond 0.00735 / 0.38 ( 6) SS BOND : angle 1.65574 / 0.86 ( 12) hydrogen bonds : bond 0.03632 / 2.29 ( 108) hydrogen bonds : angle 6.36461 / 4.14 ( 249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LEU cc_start: 0.9093 (pt) cc_final: 0.8866 (pp) REVERT: B 34 ASN cc_start: 0.9143 (m-40) cc_final: 0.8388 (p0) REVERT: B 39 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8644 (mmtt) REVERT: B 50 ASP cc_start: 0.9493 (m-30) cc_final: 0.9258 (m-30) REVERT: C 32 ASN cc_start: 0.8762 (p0) cc_final: 0.8437 (p0) REVERT: C 33 TYR cc_start: 0.9182 (m-10) cc_final: 0.8823 (m-10) REVERT: C 34 MET cc_start: 0.8918 (mtm) cc_final: 0.8665 (mtt) REVERT: C 86 THR cc_start: 0.7404 (p) cc_final: 0.6788 (p) REVERT: C 89 ASP cc_start: 0.8970 (m-30) cc_final: 0.8554 (m-30) REVERT: C 94 TYR cc_start: 0.8392 (m-10) cc_final: 0.8187 (m-10) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0546 time to fit residues: 8.2789 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3430 r_free = 0.3430 target = 0.098830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.083776 restraints weight = 11581.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.086915 restraints weight = 6638.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089085 restraints weight = 4321.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090611 restraints weight = 3044.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091683 restraints weight = 2270.386| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3405 Z= 0.150 Angle : 0.627 5.798 4630 Z= 0.332 Chirality : 0.046 0.138 491 Planarity : 0.004 0.032 601 Dihedral : 6.190 79.455 468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.64 (0.41), residues: 418 helix: -3.51 (0.67), residues: 32 sheet: 0.44 (0.47), residues: 129 loop : -0.42 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.009 0.001 TYR A 34 PHE 0.010 0.002 PHE B 71 TRP 0.012 0.002 TRP C 36 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 3399) covalent geometry : angle 0.62001 / 0.33 ( 4618) SS BOND : bond 0.00774 / 0.42 ( 6) SS BOND : angle 1.93440 / 1.00 ( 12) hydrogen bonds : bond 0.03563 / 2.30 ( 108) hydrogen bonds : angle 6.34546 / 4.18 ( 249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLN cc_start: 0.9180 (mt0) cc_final: 0.8840 (mt0) REVERT: A 177 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7465 (mtt90) REVERT: B 39 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8573 (mmtt) REVERT: B 81 GLU cc_start: 0.9368 (pm20) cc_final: 0.9060 (pm20) REVERT: C 32 ASN cc_start: 0.8754 (p0) cc_final: 0.8496 (p0) REVERT: C 33 TYR cc_start: 0.9110 (m-10) cc_final: 0.8624 (m-10) REVERT: C 34 MET cc_start: 0.8879 (mtm) cc_final: 0.8566 (mtt) REVERT: C 43 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8283 (mmmm) REVERT: C 86 THR cc_start: 0.7230 (p) cc_final: 0.6529 (p) REVERT: C 89 ASP cc_start: 0.8851 (m-30) cc_final: 0.8428 (m-30) REVERT: C 94 TYR cc_start: 0.8509 (m-10) cc_final: 0.8169 (m-10) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0446 time to fit residues: 6.8115 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3480 r_free = 0.3480 target = 0.101705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086949 restraints weight = 11392.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090154 restraints weight = 6475.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092331 restraints weight = 4163.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093830 restraints weight = 2902.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094939 restraints weight = 2161.130| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3405 Z= 0.120 Angle : 0.611 6.078 4630 Z= 0.319 Chirality : 0.046 0.154 491 Planarity : 0.003 0.031 601 Dihedral : 5.890 77.616 468 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.68 (0.41), residues: 418 helix: -3.37 (0.70), residues: 32 sheet: 0.49 (0.47), residues: 130 loop : -0.52 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 177 TYR 0.009 0.001 TYR A 34 PHE 0.011 0.001 PHE B 32 TRP 0.011 0.001 TRP C 36 HIS 0.008 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3399) covalent geometry : angle 0.60474 / 0.32 ( 4618) SS BOND : bond 0.00744 / 0.40 ( 6) SS BOND : angle 1.76810 / 0.92 ( 12) hydrogen bonds : bond 0.03414 / 2.18 ( 108) hydrogen bonds : angle 6.25976 / 4.16 ( 249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.9278 (mp10) cc_final: 0.8998 (mt0) REVERT: A 177 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7418 (mtt90) REVERT: B 39 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8593 (mmtt) REVERT: B 50 ASP cc_start: 0.9418 (m-30) cc_final: 0.9174 (m-30) REVERT: B 53 ASN cc_start: 0.9132 (m110) cc_final: 0.8731 (m-40) REVERT: B 103 LYS cc_start: 0.9284 (tppt) cc_final: 0.8938 (tppt) REVERT: C 32 ASN cc_start: 0.8942 (p0) cc_final: 0.8457 (p0) REVERT: C 33 TYR cc_start: 0.9148 (m-10) cc_final: 0.8831 (m-10) REVERT: C 34 MET cc_start: 0.8945 (mtm) cc_final: 0.8592 (mtt) REVERT: C 43 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8072 (mppt) REVERT: C 46 GLU cc_start: 0.8903 (tp30) cc_final: 0.8645 (tt0) REVERT: C 86 THR cc_start: 0.7273 (p) cc_final: 0.6559 (p) REVERT: C 89 ASP cc_start: 0.8816 (m-30) cc_final: 0.8351 (m-30) REVERT: C 94 TYR cc_start: 0.8446 (m-10) cc_final: 0.8188 (m-10) REVERT: C 98 ASP cc_start: 0.9480 (p0) cc_final: 0.9275 (p0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0484 time to fit residues: 7.7353 Evaluate side-chains 108 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.098350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084978 restraints weight = 11817.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087830 restraints weight = 6868.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089823 restraints weight = 4454.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091158 restraints weight = 3123.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092005 restraints weight = 2336.384| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3405 Z= 0.153 Angle : 0.653 7.236 4630 Z= 0.344 Chirality : 0.047 0.149 491 Planarity : 0.004 0.032 601 Dihedral : 6.201 78.522 468 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.94 (0.40), residues: 418 helix: -3.62 (0.73), residues: 26 sheet: 0.45 (0.50), residues: 108 loop : -0.78 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.011 0.002 TYR A 169 PHE 0.009 0.001 PHE A 158 TRP 0.013 0.002 TRP C 36 HIS 0.007 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 3399) covalent geometry : angle 0.64590 / 0.34 ( 4618) SS BOND : bond 0.00687 / 0.38 ( 6) SS BOND : angle 1.96160 / 1.03 ( 12) hydrogen bonds : bond 0.03757 / 2.41 ( 108) hydrogen bonds : angle 6.42615 / 4.23 ( 249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLN cc_start: 0.9256 (mt0) cc_final: 0.8993 (mt0) REVERT: A 177 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7335 (mtt90) REVERT: B 27 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7317 (mm110) REVERT: B 28 ASP cc_start: 0.8487 (p0) cc_final: 0.8252 (p0) REVERT: B 39 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8616 (mmtt) REVERT: B 50 ASP cc_start: 0.9305 (m-30) cc_final: 0.9052 (m-30) REVERT: B 53 ASN cc_start: 0.9159 (m110) cc_final: 0.8749 (m-40) REVERT: C 32 ASN cc_start: 0.8988 (p0) cc_final: 0.8441 (p0) REVERT: C 33 TYR cc_start: 0.9120 (m-10) cc_final: 0.8751 (m-10) REVERT: C 34 MET cc_start: 0.8794 (mtm) cc_final: 0.8468 (mtt) REVERT: C 86 THR cc_start: 0.7121 (p) cc_final: 0.6329 (p) REVERT: C 89 ASP cc_start: 0.8800 (m-30) cc_final: 0.8381 (m-30) REVERT: C 92 VAL cc_start: 0.8999 (m) cc_final: 0.8720 (m) REVERT: C 94 TYR cc_start: 0.8373 (m-10) cc_final: 0.8155 (m-10) REVERT: C 98 ASP cc_start: 0.9493 (p0) cc_final: 0.9267 (p0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0476 time to fit residues: 7.5434 Evaluate side-chains 104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** 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 = 0.3440 r_free = 0.3440 target = 0.099183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.085426 restraints weight = 11277.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088404 restraints weight = 6440.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090477 restraints weight = 4133.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.091874 restraints weight = 2868.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092893 restraints weight = 2126.472| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3405 Z= 0.132 Angle : 0.633 5.752 4630 Z= 0.331 Chirality : 0.047 0.148 491 Planarity : 0.004 0.030 601 Dihedral : 5.976 77.127 468 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.85 (0.40), residues: 418 helix: -3.58 (0.73), residues: 26 sheet: 0.43 (0.50), residues: 110 loop : -0.67 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.010 0.001 TYR A 34 PHE 0.007 0.001 PHE B 14 TRP 0.011 0.001 TRP C 36 HIS 0.006 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3399) covalent geometry : angle 0.62612 / 0.33 ( 4618) SS BOND : bond 0.00737 / 0.40 ( 6) SS BOND : angle 1.95793 / 1.03 ( 12) hydrogen bonds : bond 0.03602 / 2.30 ( 108) hydrogen bonds : angle 6.19764 / 4.08 ( 249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7419 (mtt90) REVERT: B 27 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7322 (mm110) REVERT: B 32 PHE cc_start: 0.8815 (m-80) cc_final: 0.8613 (m-80) REVERT: B 39 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8734 (mmtt) REVERT: B 50 ASP cc_start: 0.9265 (m-30) cc_final: 0.8995 (m-30) REVERT: B 53 ASN cc_start: 0.9137 (m110) cc_final: 0.8736 (m-40) REVERT: C 19 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6978 (ttt180) REVERT: C 32 ASN cc_start: 0.9009 (p0) cc_final: 0.8472 (p0) REVERT: C 33 TYR cc_start: 0.9106 (m-10) cc_final: 0.8855 (m-10) REVERT: C 34 MET cc_start: 0.8798 (mtm) cc_final: 0.8441 (mtt) REVERT: C 86 THR cc_start: 0.6895 (p) cc_final: 0.6038 (p) REVERT: C 89 ASP cc_start: 0.8748 (m-30) cc_final: 0.8314 (m-30) REVERT: C 92 VAL cc_start: 0.8979 (m) cc_final: 0.8776 (p) REVERT: C 94 TYR cc_start: 0.8337 (m-10) cc_final: 0.8117 (m-10) REVERT: C 98 ASP cc_start: 0.9510 (p0) cc_final: 0.9286 (p0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0441 time to fit residues: 6.9095 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086411 restraints weight = 11266.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089429 restraints weight = 6498.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091451 restraints weight = 4218.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092883 restraints weight = 2972.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093897 restraints weight = 2216.356| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3405 Z= 0.119 Angle : 0.652 8.032 4630 Z= 0.339 Chirality : 0.047 0.182 491 Planarity : 0.004 0.027 601 Dihedral : 5.851 74.303 468 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.68 (0.41), residues: 418 helix: -3.46 (0.78), residues: 26 sheet: 0.63 (0.48), residues: 120 loop : -0.65 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.014 0.001 TYR A 122 PHE 0.007 0.001 PHE B 14 TRP 0.020 0.002 TRP C 36 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3399) covalent geometry : angle 0.64499 / 0.34 ( 4618) SS BOND : bond 0.00790 / 0.41 ( 6) SS BOND : angle 2.01646 / 1.04 ( 12) hydrogen bonds : bond 0.03554 / 2.25 ( 108) hydrogen bonds : angle 6.12547 / 3.99 ( 249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7276 (mp10) REVERT: B 28 ASP cc_start: 0.8581 (p0) cc_final: 0.8326 (p0) REVERT: B 50 ASP cc_start: 0.9246 (m-30) cc_final: 0.8952 (m-30) REVERT: B 53 ASN cc_start: 0.9066 (m110) cc_final: 0.8666 (m-40) REVERT: C 32 ASN cc_start: 0.8969 (p0) cc_final: 0.8457 (p0) REVERT: C 33 TYR cc_start: 0.9068 (m-10) cc_final: 0.8738 (m-10) REVERT: C 34 MET cc_start: 0.8774 (mtm) cc_final: 0.8357 (mtt) REVERT: C 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8110 (tt0) REVERT: C 86 THR cc_start: 0.6900 (p) cc_final: 0.6075 (p) REVERT: C 89 ASP cc_start: 0.8717 (m-30) cc_final: 0.8276 (m-30) REVERT: C 94 TYR cc_start: 0.8385 (m-10) cc_final: 0.8032 (m-10) REVERT: C 98 ASP cc_start: 0.9503 (p0) cc_final: 0.9262 (p0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0444 time to fit residues: 6.7778 Evaluate side-chains 104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085445 restraints weight = 11096.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088327 restraints weight = 6443.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090331 restraints weight = 4216.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091714 restraints weight = 2980.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092702 restraints weight = 2228.082| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3405 Z= 0.128 Angle : 0.648 8.702 4630 Z= 0.334 Chirality : 0.047 0.154 491 Planarity : 0.003 0.028 601 Dihedral : 5.917 75.494 468 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.68 (0.41), residues: 418 helix: -3.51 (0.75), residues: 26 sheet: 0.62 (0.48), residues: 120 loop : -0.63 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.014 0.001 TYR A 122 PHE 0.008 0.001 PHE B 32 TRP 0.021 0.002 TRP C 36 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 3399) covalent geometry : angle 0.63960 / 0.33 ( 4618) SS BOND : bond 0.00782 / 0.41 ( 6) SS BOND : angle 2.11714 / 1.09 ( 12) hydrogen bonds : bond 0.03470 / 2.20 ( 108) hydrogen bonds : angle 6.06794 / 3.99 ( 249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7477 (mp10) REVERT: B 28 ASP cc_start: 0.8463 (p0) cc_final: 0.8218 (p0) REVERT: B 32 PHE cc_start: 0.8783 (m-80) cc_final: 0.8531 (m-80) REVERT: B 50 ASP cc_start: 0.9166 (m-30) cc_final: 0.8867 (m-30) REVERT: B 53 ASN cc_start: 0.9089 (m110) cc_final: 0.8664 (m-40) REVERT: C 32 ASN cc_start: 0.8994 (p0) cc_final: 0.8446 (p0) REVERT: C 33 TYR cc_start: 0.9124 (m-10) cc_final: 0.8790 (m-10) REVERT: C 34 MET cc_start: 0.8691 (mtm) cc_final: 0.8338 (mtt) REVERT: C 43 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8010 (mmmm) REVERT: C 46 GLU cc_start: 0.8318 (tt0) cc_final: 0.7923 (tt0) REVERT: C 86 THR cc_start: 0.6923 (p) cc_final: 0.6044 (p) REVERT: C 89 ASP cc_start: 0.8772 (m-30) cc_final: 0.8331 (m-30) REVERT: C 98 ASP cc_start: 0.9517 (p0) cc_final: 0.9280 (p0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0420 time to fit residues: 6.3267 Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085595 restraints weight = 11446.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088464 restraints weight = 6761.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090450 restraints weight = 4432.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091828 restraints weight = 3140.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092863 restraints weight = 2345.393| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3405 Z= 0.133 Angle : 0.667 8.061 4630 Z= 0.345 Chirality : 0.048 0.175 491 Planarity : 0.004 0.028 601 Dihedral : 5.910 74.709 468 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.71 (0.41), residues: 418 helix: -3.50 (0.76), residues: 26 sheet: 0.74 (0.50), residues: 109 loop : -0.67 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 18 TYR 0.014 0.001 TYR B 87 PHE 0.010 0.001 PHE B 32 TRP 0.020 0.002 TRP C 36 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3399) covalent geometry : angle 0.65994 / 0.34 ( 4618) SS BOND : bond 0.00729 / 0.39 ( 6) SS BOND : angle 2.05009 / 1.06 ( 12) hydrogen bonds : bond 0.03612 / 2.27 ( 108) hydrogen bonds : angle 6.12827 / 4.02 ( 249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 673.88 seconds wall clock time: 12 minutes 16.57 seconds (736.57 seconds total)