Starting phenix.real_space_refine on Wed Jun 4 17:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5v_37305/06_2025/8w5v_37305.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.121 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 11 5.16 5 C 2255 2.51 5 N 606 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3584 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 873 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 936 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 1 Chain: "c" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 957 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.77 Number of scatterers: 3584 At special positions: 0 Unit cell: (102, 65.28, 81.6, 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 11 16.00 O 712 8.00 N 606 7.00 C 2255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 445.9 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 11.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.829A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'c' and resid 101 through 116 removed outlier: 3.602A pdb=" N ARG c 105 " --> pdb=" O THR c 101 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU c 116 " --> pdb=" O LEU c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 127 removed outlier: 3.582A pdb=" N ASP c 126 " --> pdb=" O ILE c 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 27 removed outlier: 3.556A pdb=" N SER L 74 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 63 removed outlier: 6.651A pdb=" N TRP L 44 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR L 58 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU L 42 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 9 removed outlier: 3.970A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL H 21 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU H 86 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 72 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 63 removed outlier: 3.943A pdb=" N ILE H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR H 101 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 11 removed outlier: 3.717A pdb=" N LYS C 10 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN C 17 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 68 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG c 86 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE c 68 " --> pdb=" O ALA c 90 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL c 50 " --> pdb=" O ALA c 33 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL c 32 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL c 26 " --> pdb=" O VAL c 32 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN c 17 " --> pdb=" O LYS c 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS c 10 " --> pdb=" O GLN c 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU c 19 " --> pdb=" O LEU c 8 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 324 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: 0.82 Time building geometry restraints manager: 1.03 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: 1164 1.34 - 1.46: 777 1.46 - 1.58: 1699 1.58 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 3654 Sorted by residual: bond pdb=" C LYS H 16 " pdb=" N SER H 17 " ideal model delta sigma weight residual 1.325 1.336 -0.011 1.14e-02 7.69e+03 9.44e-01 bond pdb=" C VAL L 67 " pdb=" O VAL L 67 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.31e-01 bond pdb=" N SER H 43 " pdb=" CA SER H 43 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 7.22e-01 bond pdb=" CA SER H 17 " pdb=" CB SER H 17 " ideal model delta sigma weight residual 1.518 1.532 -0.015 2.08e-02 2.31e+03 4.92e-01 bond pdb=" C SER L 74 " pdb=" N GLY L 75 " ideal model delta sigma weight residual 1.332 1.323 0.009 1.31e-02 5.83e+03 4.43e-01 ... (remaining 3649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 4705 1.14 - 2.28: 195 2.28 - 3.42: 52 3.42 - 4.56: 10 4.56 - 5.70: 7 Bond angle restraints: 4969 Sorted by residual: angle pdb=" C SER H 17 " pdb=" CA SER H 17 " pdb=" CB SER H 17 " ideal model delta sigma weight residual 115.79 110.09 5.70 1.19e+00 7.06e-01 2.29e+01 angle pdb=" C TRP L 59 " pdb=" N ALA L 60 " pdb=" CA ALA L 60 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 angle pdb=" C SER H 43 " pdb=" CA SER H 43 " pdb=" CB SER H 43 " ideal model delta sigma weight residual 110.42 115.74 -5.32 1.99e+00 2.53e-01 7.15e+00 angle pdb=" C GLY c 39 " pdb=" N ALA c 40 " pdb=" CA ALA c 40 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 angle pdb=" C GLY C 39 " pdb=" N ALA C 40 " pdb=" CA ALA C 40 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.73e+00 ... (remaining 4964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1993 17.96 - 35.91: 160 35.91 - 53.86: 28 53.86 - 71.82: 4 71.82 - 89.77: 3 Dihedral angle restraints: 2188 sinusoidal: 825 harmonic: 1363 Sorted by residual: dihedral pdb=" CA SER H 10 " pdb=" C SER H 10 " pdb=" N GLY H 11 " pdb=" CA GLY H 11 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PRO L 11 " pdb=" C PRO L 11 " pdb=" N SER L 12 " pdb=" CA SER L 12 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ALA H 95 " pdb=" C ALA H 95 " pdb=" N VAL H 96 " pdb=" CA VAL H 96 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.53e+00 ... (remaining 2185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 318 0.025 - 0.050: 154 0.050 - 0.076: 49 0.076 - 0.101: 31 0.101 - 0.126: 22 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA VAL C 48 " pdb=" N VAL C 48 " pdb=" C VAL C 48 " pdb=" CB VAL C 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE L 57 " pdb=" N ILE L 57 " pdb=" C ILE L 57 " pdb=" CB ILE L 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE c 68 " pdb=" N ILE c 68 " pdb=" C ILE c 68 " pdb=" CB ILE c 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 571 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 11 " 0.046 5.00e-02 4.00e+02 7.07e-02 8.01e+00 pdb=" N PRO H 12 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 118 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO C 119 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 10 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO L 11 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 11 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 11 " -0.018 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 101 2.71 - 3.25: 3388 3.25 - 3.80: 4930 3.80 - 4.35: 6321 4.35 - 4.90: 11004 Nonbonded interactions: 25744 Sorted by model distance: nonbonded pdb=" O LEU c 8 " pdb=" OG1 THR c 18 " model vdw 2.157 3.040 nonbonded pdb=" OG SER L 76 " pdb=" O ASP L 79 " model vdw 2.209 3.040 nonbonded pdb=" O SER H 91 " pdb=" OG SER H 94 " model vdw 2.214 3.040 nonbonded pdb=" OG SER L 35 " pdb=" O ASN L 37 " model vdw 2.243 3.040 nonbonded pdb=" O SER C 95 " pdb=" OG SER C 95 " model vdw 2.363 3.040 ... (remaining 25739 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'c' and (resid 1 through 55 or resid 61 through 131)) } 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: 0.520 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.002 0.029 3655 Z= 0.108 Angle : 0.582 5.699 4971 Z= 0.312 Chirality : 0.041 0.126 574 Planarity : 0.005 0.071 639 Dihedral : 13.705 89.771 1309 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.38), residues: 461 helix: 0.29 (0.70), residues: 52 sheet: 0.15 (0.42), residues: 178 loop : -2.37 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 111 HIS 0.003 0.001 HIS H 38 PHE 0.006 0.001 PHE L 80 TYR 0.012 0.001 TYR L 41 ARG 0.001 0.000 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.25351 ( 121) hydrogen bonds : angle 9.31397 ( 324) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.37809 ( 2) covalent geometry : bond 0.00227 ( 3654) covalent geometry : angle 0.58225 ( 4969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.382 Fit side-chains REVERT: H 42 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: C 17 GLN cc_start: 0.8231 (mt0) cc_final: 0.7639 (mt0) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1929 time to fit residues: 17.4160 Evaluate side-chains 69 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 42 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 30.0000 chunk 11 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094955 restraints weight = 4175.868| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.53 r_work: 0.2936 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3655 Z= 0.181 Angle : 0.645 6.692 4971 Z= 0.341 Chirality : 0.045 0.155 574 Planarity : 0.005 0.057 639 Dihedral : 5.506 41.752 504 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.27 % Allowed : 12.59 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.38), residues: 461 helix: 0.03 (0.70), residues: 54 sheet: -0.02 (0.41), residues: 186 loop : -2.38 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 111 HIS 0.002 0.001 HIS H 44 PHE 0.009 0.001 PHE c 94 TYR 0.013 0.001 TYR L 41 ARG 0.002 0.000 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 121) hydrogen bonds : angle 6.06888 ( 324) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.29468 ( 2) covalent geometry : bond 0.00438 ( 3654) covalent geometry : angle 0.64475 ( 4969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.8283 (mt0) cc_final: 0.7591 (mt0) REVERT: C 52 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8907 (t) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1956 time to fit residues: 19.6358 Evaluate side-chains 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain c residue 32 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN H 6 GLN H 8 GLN H 42 GLN C 87 GLN c 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088106 restraints weight = 4276.055| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.50 r_work: 0.2855 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 3655 Z= 0.383 Angle : 0.807 7.207 4971 Z= 0.431 Chirality : 0.052 0.170 574 Planarity : 0.005 0.051 639 Dihedral : 6.545 38.854 504 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.78 % Allowed : 16.88 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.38), residues: 461 helix: -0.95 (0.65), residues: 54 sheet: -0.07 (0.40), residues: 193 loop : -2.49 (0.35), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE c 94 TYR 0.025 0.002 TYR L 41 ARG 0.006 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.06340 ( 121) hydrogen bonds : angle 5.87335 ( 324) SS BOND : bond 0.00237 ( 1) SS BOND : angle 1.30831 ( 2) covalent geometry : bond 0.00925 ( 3654) covalent geometry : angle 0.80660 ( 4969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.420 Fit side-chains REVERT: L 27 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8362 (ttmm) REVERT: H 9 GLN cc_start: 0.9008 (tt0) cc_final: 0.8664 (mt0) REVERT: C 17 GLN cc_start: 0.8403 (mt0) cc_final: 0.7987 (mt0) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 0.1901 time to fit residues: 18.7501 Evaluate side-chains 78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 8 GLN H 42 GLN C 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093728 restraints weight = 4192.571| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.52 r_work: 0.2942 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3655 Z= 0.126 Angle : 0.605 6.073 4971 Z= 0.316 Chirality : 0.043 0.149 574 Planarity : 0.004 0.047 639 Dihedral : 5.006 23.667 501 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.53 % Allowed : 19.40 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.38), residues: 461 helix: -0.41 (0.68), residues: 54 sheet: 0.46 (0.41), residues: 182 loop : -2.37 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 59 HIS 0.001 0.001 HIS H 44 PHE 0.007 0.001 PHE c 94 TYR 0.010 0.001 TYR L 58 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 121) hydrogen bonds : angle 5.35138 ( 324) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.39388 ( 2) covalent geometry : bond 0.00304 ( 3654) covalent geometry : angle 0.60550 ( 4969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.419 Fit side-chains REVERT: L 27 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8371 (ttmm) REVERT: L 46 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: H 8 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: H 9 GLN cc_start: 0.8688 (tt0) cc_final: 0.8309 (mt0) REVERT: H 30 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6084 (p90) REVERT: C 17 GLN cc_start: 0.8405 (mt0) cc_final: 0.7910 (mt0) REVERT: C 129 ASN cc_start: 0.8874 (p0) cc_final: 0.8666 (p0) REVERT: c 17 GLN cc_start: 0.8907 (mt0) cc_final: 0.8294 (mt0) REVERT: c 123 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8173 (m-30) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.1778 time to fit residues: 18.5161 Evaluate side-chains 86 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 8 GLN C 87 GLN c 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089334 restraints weight = 4277.009| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.53 r_work: 0.2874 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 3655 Z= 0.285 Angle : 0.710 6.282 4971 Z= 0.374 Chirality : 0.048 0.143 574 Planarity : 0.005 0.046 639 Dihedral : 5.467 27.404 501 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 6.30 % Allowed : 16.88 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.38), residues: 461 helix: -0.72 (0.67), residues: 54 sheet: 0.37 (0.41), residues: 183 loop : -2.45 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 59 HIS 0.002 0.001 HIS H 44 PHE 0.011 0.002 PHE c 94 TYR 0.017 0.002 TYR H 53 ARG 0.003 0.001 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 121) hydrogen bonds : angle 5.40506 ( 324) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.52594 ( 2) covalent geometry : bond 0.00692 ( 3654) covalent geometry : angle 0.71013 ( 4969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.387 Fit side-chains REVERT: L 27 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8377 (ttmm) REVERT: L 46 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8885 (tt0) REVERT: L 88 LYS cc_start: 0.6035 (mmtt) cc_final: 0.5831 (mmtm) REVERT: H 8 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: H 30 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.6868 (p90) REVERT: C 17 GLN cc_start: 0.8494 (mt0) cc_final: 0.7897 (mt0) REVERT: C 129 ASN cc_start: 0.8866 (p0) cc_final: 0.8618 (p0) REVERT: c 93 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8457 (m) REVERT: c 123 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8175 (m-30) outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.1707 time to fit residues: 18.2398 Evaluate side-chains 96 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 8 GLN H 42 GLN C 87 GLN c 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093185 restraints weight = 4256.610| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.54 r_work: 0.2928 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3655 Z= 0.130 Angle : 0.605 5.785 4971 Z= 0.315 Chirality : 0.043 0.151 574 Planarity : 0.004 0.046 639 Dihedral : 4.980 23.663 501 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.79 % Allowed : 19.14 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.39), residues: 461 helix: -0.34 (0.69), residues: 54 sheet: 0.57 (0.42), residues: 182 loop : -2.31 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 59 HIS 0.001 0.001 HIS H 44 PHE 0.007 0.001 PHE c 94 TYR 0.010 0.001 TYR L 58 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 121) hydrogen bonds : angle 5.14074 ( 324) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.25424 ( 2) covalent geometry : bond 0.00320 ( 3654) covalent geometry : angle 0.60496 ( 4969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8288 (ttmm) REVERT: H 8 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: H 30 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.6695 (p90) REVERT: H 53 TYR cc_start: 0.8921 (p90) cc_final: 0.8543 (p90) REVERT: C 17 GLN cc_start: 0.8477 (mt0) cc_final: 0.7996 (mt0) REVERT: C 129 ASN cc_start: 0.8814 (p0) cc_final: 0.8573 (p0) REVERT: c 123 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8218 (m-30) outliers start: 19 outliers final: 12 residues processed: 88 average time/residue: 0.1791 time to fit residues: 18.8707 Evaluate side-chains 88 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN C 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092420 restraints weight = 4226.561| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.54 r_work: 0.2914 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 3655 Z= 0.160 Angle : 0.614 6.946 4971 Z= 0.320 Chirality : 0.044 0.148 574 Planarity : 0.004 0.036 639 Dihedral : 4.957 23.748 501 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.54 % Allowed : 18.14 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.39), residues: 461 helix: -0.39 (0.69), residues: 54 sheet: 0.56 (0.42), residues: 182 loop : -2.32 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 59 HIS 0.002 0.001 HIS H 44 PHE 0.009 0.001 PHE c 94 TYR 0.011 0.001 TYR H 53 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 121) hydrogen bonds : angle 5.07603 ( 324) SS BOND : bond 0.00272 ( 1) SS BOND : angle 0.24692 ( 2) covalent geometry : bond 0.00399 ( 3654) covalent geometry : angle 0.61384 ( 4969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: L 20 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: L 27 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8234 (ttmm) REVERT: H 8 GLN cc_start: 0.7621 (pm20) cc_final: 0.6792 (pt0) REVERT: H 30 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.6807 (p90) REVERT: H 53 TYR cc_start: 0.8911 (p90) cc_final: 0.8479 (p90) REVERT: C 17 GLN cc_start: 0.8483 (mt0) cc_final: 0.8024 (mt0) REVERT: C 129 ASN cc_start: 0.8818 (p0) cc_final: 0.8605 (p0) REVERT: c 93 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8397 (m) REVERT: c 123 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (m-30) outliers start: 22 outliers final: 16 residues processed: 89 average time/residue: 0.1915 time to fit residues: 20.4620 Evaluate side-chains 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 32 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 36 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095507 restraints weight = 4178.408| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.55 r_work: 0.2957 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 3655 Z= 0.103 Angle : 0.572 6.435 4971 Z= 0.296 Chirality : 0.042 0.145 574 Planarity : 0.004 0.035 639 Dihedral : 4.574 20.428 501 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.03 % Allowed : 19.40 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.39), residues: 461 helix: -0.11 (0.70), residues: 54 sheet: 0.41 (0.42), residues: 189 loop : -2.16 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.007 0.001 PHE c 94 TYR 0.009 0.001 TYR L 58 ARG 0.001 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 121) hydrogen bonds : angle 4.87034 ( 324) SS BOND : bond 0.00260 ( 1) SS BOND : angle 0.16675 ( 2) covalent geometry : bond 0.00261 ( 3654) covalent geometry : angle 0.57215 ( 4969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8182 (ttmm) REVERT: H 8 GLN cc_start: 0.7625 (pm20) cc_final: 0.6824 (pt0) REVERT: H 30 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6639 (p90) REVERT: H 42 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: H 53 TYR cc_start: 0.8865 (p90) cc_final: 0.8374 (p90) REVERT: C 17 GLN cc_start: 0.8524 (mt0) cc_final: 0.8047 (mt0) REVERT: C 129 ASN cc_start: 0.8772 (p0) cc_final: 0.8541 (p0) REVERT: c 19 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8944 (pt) REVERT: c 123 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: c 129 ASN cc_start: 0.9108 (p0) cc_final: 0.8849 (p0) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.1846 time to fit residues: 19.2379 Evaluate side-chains 90 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 19 LEU Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 0.0670 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN C 87 GLN c 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090274 restraints weight = 4188.586| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.50 r_work: 0.2886 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 3655 Z= 0.242 Angle : 0.672 6.153 4971 Z= 0.354 Chirality : 0.047 0.142 574 Planarity : 0.004 0.033 639 Dihedral : 5.217 24.710 501 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 6.05 % Allowed : 17.63 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.39), residues: 461 helix: -0.46 (0.68), residues: 54 sheet: 0.44 (0.42), residues: 183 loop : -2.31 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 59 HIS 0.002 0.001 HIS H 44 PHE 0.011 0.001 PHE c 94 TYR 0.015 0.002 TYR H 53 ARG 0.003 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 121) hydrogen bonds : angle 5.11061 ( 324) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.45066 ( 2) covalent geometry : bond 0.00590 ( 3654) covalent geometry : angle 0.67166 ( 4969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8256 (ttmm) REVERT: H 8 GLN cc_start: 0.7740 (pm20) cc_final: 0.7116 (pt0) REVERT: H 30 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7187 (p90) REVERT: C 17 GLN cc_start: 0.8504 (mt0) cc_final: 0.8035 (mt0) REVERT: C 129 ASN cc_start: 0.8864 (p0) cc_final: 0.8620 (p0) REVERT: c 93 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8425 (m) REVERT: c 123 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8178 (m-30) outliers start: 24 outliers final: 17 residues processed: 94 average time/residue: 0.1774 time to fit residues: 20.1497 Evaluate side-chains 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 0.0870 chunk 26 optimal weight: 0.0030 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.6970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN C 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096573 restraints weight = 4143.542| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.54 r_work: 0.2978 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 3655 Z= 0.104 Angle : 0.581 7.946 4971 Z= 0.302 Chirality : 0.042 0.140 574 Planarity : 0.004 0.036 639 Dihedral : 4.574 19.116 501 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.02 % Allowed : 20.40 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.39), residues: 461 helix: -0.11 (0.71), residues: 54 sheet: 0.33 (0.42), residues: 189 loop : -2.16 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.005 0.001 PHE c 94 TYR 0.009 0.001 TYR L 58 ARG 0.002 0.000 ARG c 24 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 121) hydrogen bonds : angle 4.81476 ( 324) SS BOND : bond 0.00297 ( 1) SS BOND : angle 0.34420 ( 2) covalent geometry : bond 0.00266 ( 3654) covalent geometry : angle 0.58111 ( 4969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8212 (ttmm) REVERT: L 88 LYS cc_start: 0.6274 (mmtt) cc_final: 0.5882 (mmtt) REVERT: H 8 GLN cc_start: 0.7600 (pm20) cc_final: 0.6984 (pt0) REVERT: H 30 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6793 (p90) REVERT: H 42 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: H 53 TYR cc_start: 0.8859 (p90) cc_final: 0.8459 (p90) REVERT: H 84 MET cc_start: 0.8281 (ptt) cc_final: 0.7929 (ptm) REVERT: C 17 GLN cc_start: 0.8529 (mt0) cc_final: 0.8058 (mt0) REVERT: C 129 ASN cc_start: 0.8778 (p0) cc_final: 0.8557 (p0) REVERT: c 129 ASN cc_start: 0.9095 (p0) cc_final: 0.8856 (p0) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1899 time to fit residues: 18.6618 Evaluate side-chains 84 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN C 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.097277 restraints weight = 4160.660| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.55 r_work: 0.2963 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 3655 Z= 0.110 Angle : 0.578 7.512 4971 Z= 0.300 Chirality : 0.042 0.138 574 Planarity : 0.004 0.038 639 Dihedral : 4.484 19.180 501 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.03 % Allowed : 19.65 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.39), residues: 461 helix: -0.01 (0.71), residues: 54 sheet: 0.32 (0.42), residues: 189 loop : -2.13 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 59 HIS 0.002 0.000 HIS H 38 PHE 0.007 0.001 PHE c 94 TYR 0.009 0.001 TYR L 58 ARG 0.001 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 121) hydrogen bonds : angle 4.74447 ( 324) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.43584 ( 2) covalent geometry : bond 0.00285 ( 3654) covalent geometry : angle 0.57778 ( 4969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.11 seconds wall clock time: 41 minutes 3.86 seconds (2463.86 seconds total)