Starting phenix.real_space_refine on Fri Oct 10 11:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5v_37305/10_2025/8w5v_37305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5v_37305/10_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_37305/10_2025/8w5v_37305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5v_37305/10_2025/8w5v_37305.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5v_37305/10_2025/8w5v_37305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5v_37305/10_2025/8w5v_37305.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.50, per 1000 atoms: 0.42 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: 0.29 Conformation dependent library (CDL) restraints added in 202.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.17 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: 0.50 Time building geometry restraints manager: 0.49 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: 0.710 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG H 77 TYR 0.012 0.001 TYR L 41 PHE 0.006 0.001 PHE L 80 TRP 0.016 0.001 TRP H 111 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3654) covalent geometry : angle 0.58225 ( 4969) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.37809 ( 2) hydrogen bonds : bond 0.25351 ( 121) hydrogen bonds : angle 9.31397 ( 324) *********************** 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 : 0.171 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: 0.0961 time to fit residues: 8.5873 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 : 0.127 ------------------------------------------------------------------------------- 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 24 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.135208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094849 restraints weight = 4211.702| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.55 r_work: 0.2944 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1254 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= 0.158 Angle : 0.625 6.559 4971 Z= 0.330 Chirality : 0.044 0.151 574 Planarity : 0.005 0.057 639 Dihedral : 5.370 41.148 504 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.76 % Allowed : 12.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.38), residues: 461 helix: 0.13 (0.70), residues: 54 sheet: 0.01 (0.41), residues: 186 loop : -2.36 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 47 TYR 0.012 0.001 TYR L 41 PHE 0.009 0.001 PHE c 94 TRP 0.013 0.001 TRP H 111 HIS 0.001 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3654) covalent geometry : angle 0.62516 ( 4969) SS BOND : bond 0.00308 ( 1) SS BOND : angle 0.32048 ( 2) hydrogen bonds : bond 0.05196 ( 121) hydrogen bonds : angle 6.14258 ( 324) *********************** 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 88 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: H 8 GLN cc_start: 0.8060 (pm20) cc_final: 0.7532 (pt0) REVERT: H 53 TYR cc_start: 0.8925 (p90) cc_final: 0.8582 (p90) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.0872 time to fit residues: 8.5160 Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 VAL 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 32 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094785 restraints weight = 4214.120| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.53 r_work: 0.2954 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3655 Z= 0.145 Angle : 0.606 6.037 4971 Z= 0.318 Chirality : 0.044 0.150 574 Planarity : 0.004 0.049 639 Dihedral : 5.380 38.966 504 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.27 % Allowed : 16.62 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.38), residues: 461 helix: -0.09 (0.69), residues: 54 sheet: 0.22 (0.41), residues: 189 loop : -2.33 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 70 TYR 0.010 0.001 TYR H 53 PHE 0.009 0.001 PHE c 94 TRP 0.014 0.001 TRP H 111 HIS 0.001 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3654) covalent geometry : angle 0.60624 ( 4969) SS BOND : bond 0.00540 ( 1) SS BOND : angle 0.89918 ( 2) hydrogen bonds : bond 0.04267 ( 121) hydrogen bonds : angle 5.43198 ( 324) *********************** 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: 13 poor density : 76 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: L 27 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8353 (ttmm) REVERT: H 53 TYR cc_start: 0.8940 (p90) cc_final: 0.8502 (p90) REVERT: C 17 GLN cc_start: 0.8391 (mt0) cc_final: 0.7826 (mt0) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.0788 time to fit residues: 7.8135 Evaluate side-chains 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 L residue 85 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090357 restraints weight = 4261.073| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.50 r_work: 0.2889 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 3655 Z= 0.266 Angle : 0.700 6.463 4971 Z= 0.371 Chirality : 0.047 0.149 574 Planarity : 0.005 0.045 639 Dihedral : 5.991 41.894 504 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.03 % Allowed : 17.63 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.38), residues: 461 helix: -0.51 (0.67), residues: 54 sheet: 0.47 (0.41), residues: 183 loop : -2.40 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 70 TYR 0.017 0.002 TYR H 53 PHE 0.013 0.001 PHE c 94 TRP 0.013 0.002 TRP H 111 HIS 0.002 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 3654) covalent geometry : angle 0.69962 ( 4969) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.88410 ( 2) hydrogen bonds : bond 0.05166 ( 121) hydrogen bonds : angle 5.45462 ( 324) *********************** 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 91 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.178 Fit side-chains REVERT: H 9 GLN cc_start: 0.8794 (tt0) cc_final: 0.8458 (mt0) REVERT: C 17 GLN cc_start: 0.8330 (mt0) cc_final: 0.7780 (mt0) REVERT: c 93 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8405 (m) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.0782 time to fit residues: 7.8721 Evaluate side-chains 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 L residue 87 VAL Chi-restraints excluded: chain H residue 37 LEU 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 80 CYS Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095988 restraints weight = 4157.486| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.55 r_work: 0.2951 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2165 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= 0.106 Angle : 0.579 6.347 4971 Z= 0.300 Chirality : 0.043 0.143 574 Planarity : 0.004 0.041 639 Dihedral : 4.623 21.607 501 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.78 % Allowed : 19.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.39), residues: 461 helix: -0.20 (0.69), residues: 54 sheet: 0.45 (0.42), residues: 189 loop : -2.20 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.009 0.001 TYR H 63 PHE 0.006 0.001 PHE c 94 TRP 0.004 0.000 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3654) covalent geometry : angle 0.57920 ( 4969) SS BOND : bond 0.00241 ( 1) SS BOND : angle 0.27425 ( 2) hydrogen bonds : bond 0.03455 ( 121) hydrogen bonds : angle 5.04544 ( 324) *********************** 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 89 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.206 Fit side-chains REVERT: L 27 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8313 (ttmm) REVERT: H 8 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: H 9 GLN cc_start: 0.8615 (tt0) cc_final: 0.8306 (mt0) REVERT: H 30 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.6160 (p90) REVERT: H 53 TYR cc_start: 0.8794 (p90) cc_final: 0.8352 (p90) REVERT: C 17 GLN cc_start: 0.8290 (mt0) cc_final: 0.7718 (mt0) REVERT: c 129 ASN cc_start: 0.9048 (p0) cc_final: 0.8819 (p0) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.0790 time to fit residues: 7.6450 Evaluate side-chains 82 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL 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 70 LYS Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 80 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.0270 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 40 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097772 restraints weight = 4104.274| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.56 r_work: 0.2992 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 3655 Z= 0.097 Angle : 0.567 6.989 4971 Z= 0.292 Chirality : 0.042 0.142 574 Planarity : 0.004 0.038 639 Dihedral : 4.375 21.026 501 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.77 % Allowed : 19.40 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.40), residues: 461 helix: -0.01 (0.70), residues: 54 sheet: 0.58 (0.42), residues: 189 loop : -2.10 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 63 TYR 0.009 0.001 TYR L 58 PHE 0.007 0.001 PHE c 94 TRP 0.005 0.001 TRP L 59 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3654) covalent geometry : angle 0.56731 ( 4969) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.44284 ( 2) hydrogen bonds : bond 0.03141 ( 121) hydrogen bonds : angle 4.88338 ( 324) *********************** 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 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: H 8 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: H 30 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.6022 (p90) REVERT: H 53 TYR cc_start: 0.8759 (p90) cc_final: 0.8400 (p90) REVERT: C 17 GLN cc_start: 0.8341 (mt0) cc_final: 0.7782 (mt0) REVERT: c 93 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8353 (m) REVERT: c 129 ASN cc_start: 0.9027 (p0) cc_final: 0.8793 (p0) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.0834 time to fit residues: 7.5280 Evaluate side-chains 80 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 6 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 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 20 VAL Chi-restraints excluded: chain c residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 8 GLN C 87 GLN C 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090144 restraints weight = 4300.538| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.53 r_work: 0.2884 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 3655 Z= 0.296 Angle : 0.710 5.956 4971 Z= 0.373 Chirality : 0.048 0.140 574 Planarity : 0.005 0.038 639 Dihedral : 5.227 26.541 501 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 5.54 % Allowed : 16.88 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.39), residues: 461 helix: -0.48 (0.67), residues: 54 sheet: 0.32 (0.42), residues: 190 loop : -2.27 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 109 TYR 0.018 0.002 TYR H 53 PHE 0.011 0.002 PHE c 94 TRP 0.013 0.002 TRP L 59 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00717 ( 3654) covalent geometry : angle 0.71037 ( 4969) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.63639 ( 2) hydrogen bonds : bond 0.05066 ( 121) hydrogen bonds : angle 5.16770 ( 324) *********************** 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 90 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.127 Fit side-chains REVERT: L 27 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8361 (ttmm) REVERT: L 46 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: H 8 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: H 30 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6381 (p90) REVERT: C 17 GLN cc_start: 0.8342 (mt0) cc_final: 0.7807 (mt0) REVERT: c 123 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8180 (m-30) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 0.0816 time to fit residues: 8.0415 Evaluate side-chains 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 87 VAL 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 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 129 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094753 restraints weight = 4221.670| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.55 r_work: 0.2951 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 3655 Z= 0.110 Angle : 0.588 6.219 4971 Z= 0.305 Chirality : 0.043 0.147 574 Planarity : 0.004 0.040 639 Dihedral : 4.716 21.918 501 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.53 % Allowed : 19.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.40), residues: 461 helix: -0.14 (0.70), residues: 54 sheet: 0.49 (0.42), residues: 189 loop : -2.13 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.009 0.001 TYR H 63 PHE 0.007 0.001 PHE c 94 TRP 0.007 0.001 TRP H 50 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3654) covalent geometry : angle 0.58775 ( 4969) SS BOND : bond 0.00288 ( 1) SS BOND : angle 0.30338 ( 2) hydrogen bonds : bond 0.03473 ( 121) hydrogen bonds : angle 4.96508 ( 324) *********************** 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 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: H 8 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: H 30 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.6230 (p90) REVERT: H 53 TYR cc_start: 0.8824 (p90) cc_final: 0.8322 (p90) REVERT: C 17 GLN cc_start: 0.8376 (mt0) cc_final: 0.7822 (mt0) REVERT: c 93 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8394 (m) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.0810 time to fit residues: 7.6127 Evaluate side-chains 78 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 VAL 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 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095270 restraints weight = 4100.386| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.53 r_work: 0.2959 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 3655 Z= 0.114 Angle : 0.582 7.628 4971 Z= 0.302 Chirality : 0.042 0.144 574 Planarity : 0.004 0.039 639 Dihedral : 4.545 21.093 501 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.77 % Allowed : 19.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.39), residues: 461 helix: -0.02 (0.71), residues: 54 sheet: 0.47 (0.42), residues: 189 loop : -2.12 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 70 TYR 0.009 0.001 TYR L 58 PHE 0.008 0.001 PHE c 94 TRP 0.006 0.001 TRP H 50 HIS 0.001 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3654) covalent geometry : angle 0.58204 ( 4969) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.29809 ( 2) hydrogen bonds : bond 0.03392 ( 121) hydrogen bonds : angle 4.86421 ( 324) *********************** 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 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: H 8 GLN cc_start: 0.7443 (pm20) cc_final: 0.6653 (pt0) REVERT: H 30 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.6311 (p90) REVERT: H 53 TYR cc_start: 0.8749 (p90) cc_final: 0.8283 (p90) REVERT: C 17 GLN cc_start: 0.8352 (mt0) cc_final: 0.7804 (mt0) REVERT: c 93 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8364 (m) REVERT: c 123 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8186 (m-30) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0829 time to fit residues: 7.3305 Evaluate side-chains 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 24 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.136264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095753 restraints weight = 4210.355| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.58 r_work: 0.2969 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 3655 Z= 0.110 Angle : 0.572 7.422 4971 Z= 0.296 Chirality : 0.042 0.142 574 Planarity : 0.004 0.038 639 Dihedral : 4.395 19.478 501 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.02 % Allowed : 20.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.39), residues: 461 helix: 0.08 (0.71), residues: 54 sheet: 0.44 (0.41), residues: 189 loop : -2.10 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 63 TYR 0.009 0.001 TYR L 58 PHE 0.007 0.001 PHE c 94 TRP 0.005 0.001 TRP H 50 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3654) covalent geometry : angle 0.57161 ( 4969) SS BOND : bond 0.00260 ( 1) SS BOND : angle 0.38300 ( 2) hydrogen bonds : bond 0.03242 ( 121) hydrogen bonds : angle 4.71285 ( 324) ********************** 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 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: L 88 LYS cc_start: 0.6494 (mmtt) cc_final: 0.6141 (mmtt) REVERT: H 8 GLN cc_start: 0.7400 (pm20) cc_final: 0.6854 (pt0) REVERT: H 30 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.6222 (p90) REVERT: H 53 TYR cc_start: 0.8717 (p90) cc_final: 0.8159 (p90) REVERT: C 17 GLN cc_start: 0.8331 (mt0) cc_final: 0.7761 (mt0) REVERT: c 93 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8360 (m) REVERT: c 123 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (m-30) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.0858 time to fit residues: 7.7442 Evaluate side-chains 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 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 43 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 2.6384 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.133573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093326 restraints weight = 4186.966| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.54 r_work: 0.2932 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 3655 Z= 0.164 Angle : 0.608 7.050 4971 Z= 0.318 Chirality : 0.044 0.139 574 Planarity : 0.004 0.039 639 Dihedral : 4.668 21.568 501 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.39), residues: 461 helix: -0.10 (0.71), residues: 54 sheet: 0.41 (0.41), residues: 189 loop : -2.15 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.012 0.001 TYR H 53 PHE 0.009 0.001 PHE c 94 TRP 0.009 0.001 TRP L 59 HIS 0.001 0.000 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3654) covalent geometry : angle 0.60841 ( 4969) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.38410 ( 2) hydrogen bonds : bond 0.03907 ( 121) hydrogen bonds : angle 4.81312 ( 324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1193.60 seconds wall clock time: 21 minutes 14.73 seconds (1274.73 seconds total)