Starting phenix.real_space_refine on Fri May 9 19:45:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5v_37305/05_2025/8w5v_37305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5v_37305/05_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_37305/05_2025/8w5v_37305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5v_37305/05_2025/8w5v_37305.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5v_37305/05_2025/8w5v_37305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5v_37305/05_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-5687/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: 2.61, per 1000 atoms: 0.73 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: 0.79 Conformation dependent library (CDL) restraints added in 412.2 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: 0.46 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: 0.84 Time building geometry restraints manager: 0.94 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- 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 : 0.433 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: 0.1914 time to fit residues: 17.2665 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 : 0.383 ------------------------------------------------------------------------------- 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 = 0.135253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094964 restraints weight = 4175.863| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.53 r_work: 0.2922 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 6.06890 ( 324) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.29473 ( 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 : 0.389 Fit side-chains revert: symmetry clash REVERT: C 17 GLN cc_start: 0.8295 (mt0) cc_final: 0.7606 (mt0) REVERT: C 52 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8907 (t) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1890 time to fit residues: 18.9299 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 : 0.403 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.128392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088576 restraints weight = 4263.352| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.50 r_work: 0.2850 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2199 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= 0.366 Angle : 0.790 7.146 4971 Z= 0.421 Chirality : 0.051 0.166 574 Planarity : 0.005 0.052 639 Dihedral : 6.425 39.163 504 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: -1.83 (0.38), residues: 461 helix: -0.87 (0.65), residues: 54 sheet: -0.04 (0.40), residues: 193 loop : -2.48 (0.35), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.002 0.001 HIS H 44 PHE 0.015 0.002 PHE c 94 TYR 0.024 0.002 TYR L 41 ARG 0.006 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.06169 ( 121) hydrogen bonds : angle 5.84377 ( 324) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.92173 ( 2) covalent geometry : bond 0.00883 ( 3654) covalent geometry : angle 0.78977 ( 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 88 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.405 Fit side-chains REVERT: L 27 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8375 (ttmm) REVERT: H 9 GLN cc_start: 0.8958 (tt0) cc_final: 0.8598 (mt0) REVERT: C 17 GLN cc_start: 0.8402 (mt0) cc_final: 0.8001 (mt0) REVERT: c 93 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8428 (m) outliers start: 15 outliers final: 8 residues processed: 82 average time/residue: 0.1800 time to fit residues: 17.5824 Evaluate side-chains 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.134812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094679 restraints weight = 4178.988| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.53 r_work: 0.2952 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 3655 Z= 0.114 Angle : 0.591 5.917 4971 Z= 0.308 Chirality : 0.043 0.146 574 Planarity : 0.004 0.046 639 Dihedral : 4.855 22.758 501 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.27 % Allowed : 19.40 % Favored : 77.33 % 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: -1.35 (0.38), residues: 461 helix: -0.30 (0.69), residues: 54 sheet: 0.50 (0.41), residues: 182 loop : -2.34 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 50 HIS 0.001 0.000 HIS H 38 PHE 0.005 0.001 PHE c 94 TYR 0.010 0.001 TYR H 97 ARG 0.002 0.000 ARG c 24 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 121) hydrogen bonds : angle 5.29153 ( 324) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.34555 ( 2) covalent geometry : bond 0.00282 ( 3654) covalent geometry : angle 0.59092 ( 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 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8348 (ttmm) REVERT: H 8 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7339 (pt0) REVERT: H 30 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.6024 (p90) REVERT: H 53 TYR cc_start: 0.8915 (p90) cc_final: 0.8514 (p90) REVERT: C 17 GLN cc_start: 0.8412 (mt0) cc_final: 0.7897 (mt0) REVERT: C 129 ASN cc_start: 0.8851 (p0) cc_final: 0.8616 (p0) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.1770 time to fit residues: 17.9951 Evaluate side-chains 84 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL 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 c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 80 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.128083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.088083 restraints weight = 4328.834| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.53 r_work: 0.2852 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 3655 Z= 0.344 Angle : 0.756 6.497 4971 Z= 0.398 Chirality : 0.050 0.144 574 Planarity : 0.005 0.046 639 Dihedral : 5.659 28.503 501 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 5.79 % Allowed : 17.63 % 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: -1.72 (0.38), residues: 461 helix: -0.90 (0.65), residues: 54 sheet: 0.11 (0.41), residues: 193 loop : -2.46 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 59 HIS 0.002 0.001 HIS H 44 PHE 0.012 0.002 PHE c 94 TYR 0.020 0.002 TYR H 53 ARG 0.005 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.05697 ( 121) hydrogen bonds : angle 5.48397 ( 324) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.64168 ( 2) covalent geometry : bond 0.00832 ( 3654) covalent geometry : angle 0.75578 ( 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 97 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.431 Fit side-chains REVERT: L 27 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8379 (ttmm) REVERT: L 88 LYS cc_start: 0.6136 (mmtt) cc_final: 0.5922 (mmtm) REVERT: H 30 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.6986 (p90) REVERT: H 97 TYR cc_start: 0.8594 (m-10) cc_final: 0.8377 (m-80) REVERT: C 17 GLN cc_start: 0.8515 (mt0) cc_final: 0.8185 (mt0) REVERT: C 129 ASN cc_start: 0.8964 (p0) cc_final: 0.8727 (p0) REVERT: c 93 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8472 (m) REVERT: c 123 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8199 (m-30) outliers start: 23 outliers final: 15 residues processed: 85 average time/residue: 0.1800 time to fit residues: 18.3662 Evaluate side-chains 91 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093856 restraints weight = 4241.615| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.54 r_work: 0.2948 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3655 Z= 0.117 Angle : 0.593 5.792 4971 Z= 0.308 Chirality : 0.043 0.150 574 Planarity : 0.004 0.044 639 Dihedral : 4.932 21.847 501 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.78 % Allowed : 20.15 % 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: -1.31 (0.39), residues: 461 helix: -0.36 (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 0.005 0.001 TRP H 50 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.001 PHE H 67 TYR 0.010 0.001 TYR L 58 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 121) hydrogen bonds : angle 5.07304 ( 324) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.25146 ( 2) covalent geometry : bond 0.00285 ( 3654) covalent geometry : angle 0.59310 ( 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 94 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: H 8 GLN cc_start: 0.7655 (pm20) cc_final: 0.7097 (pt0) REVERT: H 30 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6734 (p90) REVERT: H 53 TYR cc_start: 0.8896 (p90) cc_final: 0.8534 (p90) REVERT: C 17 GLN cc_start: 0.8457 (mt0) cc_final: 0.7955 (mt0) REVERT: C 129 ASN cc_start: 0.8874 (p0) cc_final: 0.8652 (p0) REVERT: c 123 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (m-30) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.1705 time to fit residues: 17.9438 Evaluate side-chains 88 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.134303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093946 restraints weight = 4204.666| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.55 r_work: 0.2949 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 3655 Z= 0.116 Angle : 0.584 6.777 4971 Z= 0.304 Chirality : 0.043 0.146 574 Planarity : 0.004 0.036 639 Dihedral : 4.706 21.442 501 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.28 % Allowed : 18.89 % 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: -1.19 (0.39), residues: 461 helix: -0.20 (0.70), residues: 54 sheet: 0.65 (0.42), residues: 182 loop : -2.29 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 59 HIS 0.003 0.001 HIS H 44 PHE 0.008 0.001 PHE c 94 TYR 0.009 0.001 TYR L 58 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 121) hydrogen bonds : angle 4.93918 ( 324) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.24631 ( 2) covalent geometry : bond 0.00297 ( 3654) covalent geometry : angle 0.58449 ( 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 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8206 (ttmm) REVERT: H 8 GLN cc_start: 0.7632 (pm20) cc_final: 0.7027 (pt0) REVERT: H 30 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.6684 (p90) REVERT: H 53 TYR cc_start: 0.8870 (p90) cc_final: 0.8387 (p90) REVERT: C 17 GLN cc_start: 0.8528 (mt0) cc_final: 0.8061 (mt0) REVERT: C 129 ASN cc_start: 0.8858 (p0) cc_final: 0.8640 (p0) REVERT: c 123 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8213 (m-30) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.1760 time to fit residues: 18.4922 Evaluate side-chains 91 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 87 VAL 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 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: 0.9980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 40 optimal weight: 0.0770 overall best weight: 2.3542 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.133209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093181 restraints weight = 4202.756| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.52 r_work: 0.2928 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 3655 Z= 0.151 Angle : 0.601 6.280 4971 Z= 0.314 Chirality : 0.044 0.144 574 Planarity : 0.004 0.034 639 Dihedral : 4.795 22.238 501 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.29 % Allowed : 17.88 % 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: -1.23 (0.39), residues: 461 helix: -0.28 (0.70), residues: 54 sheet: 0.65 (0.42), residues: 182 loop : -2.32 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.03811 ( 121) hydrogen bonds : angle 4.94463 ( 324) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.29888 ( 2) covalent geometry : bond 0.00378 ( 3654) covalent geometry : angle 0.60123 ( 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 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: L 20 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5685 (mp0) REVERT: L 27 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8235 (ttmm) REVERT: H 8 GLN cc_start: 0.7679 (pm20) cc_final: 0.7096 (pt0) REVERT: H 30 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6758 (p90) REVERT: C 17 GLN cc_start: 0.8553 (mt0) cc_final: 0.8080 (mt0) REVERT: C 129 ASN cc_start: 0.8823 (p0) cc_final: 0.8568 (p0) REVERT: c 123 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8206 (m-30) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.1780 time to fit residues: 18.3125 Evaluate side-chains 89 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.130511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090402 restraints weight = 4179.075| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.51 r_work: 0.2888 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 3655 Z= 0.241 Angle : 0.677 6.890 4971 Z= 0.356 Chirality : 0.046 0.141 574 Planarity : 0.004 0.033 639 Dihedral : 5.242 24.949 501 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.24 % Favored : 91.54 % Rotamer: Outliers : 5.29 % Allowed : 17.88 % 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: -1.45 (0.39), residues: 461 helix: -0.60 (0.67), residues: 54 sheet: 0.45 (0.42), residues: 183 loop : -2.38 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 L 63 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 121) hydrogen bonds : angle 5.15131 ( 324) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.57912 ( 2) covalent geometry : bond 0.00591 ( 3654) covalent geometry : angle 0.67674 ( 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 95 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8254 (ttmm) REVERT: H 8 GLN cc_start: 0.7636 (pm20) cc_final: 0.7111 (pt0) REVERT: H 30 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7177 (p90) REVERT: C 17 GLN cc_start: 0.8515 (mt0) cc_final: 0.8055 (mt0) REVERT: C 129 ASN cc_start: 0.8867 (p0) cc_final: 0.8624 (p0) REVERT: c 93 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8426 (m) REVERT: c 123 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8229 (m-30) outliers start: 21 outliers final: 16 residues processed: 87 average time/residue: 0.1841 time to fit residues: 19.1675 Evaluate side-chains 93 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.4912 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096554 restraints weight = 4138.497| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.55 r_work: 0.2998 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 3655 Z= 0.099 Angle : 0.579 7.314 4971 Z= 0.299 Chirality : 0.042 0.140 574 Planarity : 0.004 0.038 639 Dihedral : 4.545 18.914 501 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.27 % Allowed : 19.65 % 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: -1.32 (0.39), residues: 461 helix: -0.11 (0.71), residues: 54 sheet: 0.31 (0.41), residues: 189 loop : -2.24 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.006 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 0.03008 ( 121) hydrogen bonds : angle 4.83279 ( 324) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.32058 ( 2) covalent geometry : bond 0.00254 ( 3654) covalent geometry : angle 0.57913 ( 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 85 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8269 (ttmm) REVERT: L 88 LYS cc_start: 0.6363 (mmtt) cc_final: 0.5965 (mmtt) REVERT: H 8 GLN cc_start: 0.7595 (pm20) cc_final: 0.7018 (pt0) REVERT: H 30 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6632 (p90) REVERT: H 42 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: H 53 TYR cc_start: 0.8801 (p90) cc_final: 0.8233 (p90) REVERT: C 17 GLN cc_start: 0.8540 (mt0) cc_final: 0.8083 (mt0) REVERT: C 129 ASN cc_start: 0.8791 (p0) cc_final: 0.8567 (p0) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.1826 time to fit residues: 17.4302 Evaluate side-chains 82 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 87 VAL 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 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 80 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094176 restraints weight = 4203.626| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.54 r_work: 0.2951 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 3655 Z= 0.134 Angle : 0.597 6.921 4971 Z= 0.312 Chirality : 0.043 0.138 574 Planarity : 0.004 0.037 639 Dihedral : 4.609 20.602 501 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.53 % Allowed : 18.64 % 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: -1.34 (0.39), residues: 461 helix: -0.09 (0.71), residues: 54 sheet: 0.30 (0.41), residues: 189 loop : -2.28 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 59 HIS 0.001 0.000 HIS H 38 PHE 0.008 0.001 PHE c 94 TYR 0.010 0.001 TYR H 53 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 121) hydrogen bonds : angle 4.80762 ( 324) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.41756 ( 2) covalent geometry : bond 0.00338 ( 3654) covalent geometry : angle 0.59713 ( 4969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.51 seconds wall clock time: 40 minutes 24.34 seconds (2424.34 seconds total)