Starting phenix.real_space_refine on Fri Aug 22 13:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5p_37300/08_2025/8w5p_37300.map" } resolution = 3.3 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= 0.106 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 2251 2.51 5 N 606 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3582 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: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 935 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain breaks: 1 Chain: "c" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 956 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 Time building chain proxies: 1.11, per 1000 atoms: 0.31 Number of scatterers: 3582 At special positions: 0 Unit cell: (97.68, 63.36, 80.52, 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 714 8.00 N 606 7.00 C 2251 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: 0.27 Conformation dependent library (CDL) restraints added in 133.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 5 helices and 5 sheets defined 10.8% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.751A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'c' and resid 41 through 45 removed outlier: 4.261A pdb=" N GLU c 45 " --> pdb=" O PRO c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 101 through 116 Processing helix chain 'c' and resid 118 through 125 removed outlier: 3.538A pdb=" N ASP c 123 " --> pdb=" O PRO c 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 7 through 9 removed outlier: 3.620A pdb=" N THR L 72 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 62 through 63 removed outlier: 6.527A pdb=" N TRP L 44 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR L 58 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 6.709A 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 8 removed outlier: 3.641A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 97 through 102 removed outlier: 7.473A pdb=" N TYR H 97 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN H 113 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS H 99 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP H 111 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.193A 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: 6.001A pdb=" N GLN C 17 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG c 86 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER c 34 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN c 17 " --> pdb=" O ASN c 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN c 10 " --> pdb=" O GLN c 17 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 321 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: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 601 1.30 - 1.42: 925 1.42 - 1.55: 2111 1.55 - 1.68: 1 1.68 - 1.81: 14 Bond restraints: 3652 Sorted by residual: bond pdb=" C TRP H 50 " pdb=" O TRP H 50 " ideal model delta sigma weight residual 1.234 1.168 0.066 1.24e-02 6.50e+03 2.83e+01 bond pdb=" C GLU H 49 " pdb=" O GLU H 49 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.28e-02 6.10e+03 2.79e+01 bond pdb=" C ILE H 51 " pdb=" O ILE H 51 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.45e-02 4.76e+03 1.35e+01 bond pdb=" CB TRP H 50 " pdb=" CG TRP H 50 " ideal model delta sigma weight residual 1.498 1.387 0.111 3.10e-02 1.04e+03 1.29e+01 bond pdb=" C LEU H 48 " pdb=" O LEU H 48 " ideal model delta sigma weight residual 1.234 1.192 0.043 1.22e-02 6.72e+03 1.21e+01 ... (remaining 3647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 4793 1.82 - 3.64: 146 3.64 - 5.46: 24 5.46 - 7.27: 5 7.27 - 9.09: 1 Bond angle restraints: 4969 Sorted by residual: angle pdb=" N TRP H 50 " pdb=" CA TRP H 50 " pdb=" CB TRP H 50 " ideal model delta sigma weight residual 110.04 103.78 6.26 1.47e+00 4.63e-01 1.81e+01 angle pdb=" N TRP H 50 " pdb=" CA TRP H 50 " pdb=" C TRP H 50 " ideal model delta sigma weight residual 110.35 115.13 -4.78 1.36e+00 5.41e-01 1.23e+01 angle pdb=" C GLU H 46 " pdb=" N SER H 47 " pdb=" CA SER H 47 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N SER H 47 " pdb=" CA SER H 47 " pdb=" C SER H 47 " ideal model delta sigma weight residual 110.80 117.84 -7.04 2.13e+00 2.20e-01 1.09e+01 angle pdb=" N GLU H 49 " pdb=" CA GLU H 49 " pdb=" C GLU H 49 " ideal model delta sigma weight residual 109.40 114.75 -5.35 1.63e+00 3.76e-01 1.08e+01 ... (remaining 4964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1956 15.93 - 31.85: 177 31.85 - 47.78: 38 47.78 - 63.71: 9 63.71 - 79.63: 4 Dihedral angle restraints: 2184 sinusoidal: 821 harmonic: 1363 Sorted by residual: dihedral pdb=" CA GLN L 98 " pdb=" C GLN L 98 " pdb=" N GLN L 99 " pdb=" CA GLN L 99 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU H 49 " pdb=" CB GLU H 49 " pdb=" CG GLU H 49 " pdb=" CD GLU H 49 " ideal model delta sinusoidal sigma weight residual -180.00 -120.87 -59.13 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS C 16 " pdb=" CD LYS C 16 " pdb=" CE LYS C 16 " pdb=" NZ LYS C 16 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 2181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 487 0.063 - 0.127: 79 0.127 - 0.190: 6 0.190 - 0.253: 1 0.253 - 0.317: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA SER H 47 " pdb=" N SER H 47 " pdb=" C SER H 47 " pdb=" CB SER H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB THR c 93 " pdb=" CA THR c 93 " pdb=" OG1 THR c 93 " pdb=" CG2 THR c 93 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR L 83 " pdb=" CA THR L 83 " pdb=" OG1 THR L 83 " pdb=" CG2 THR L 83 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 571 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 46 " 0.025 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C GLU H 46 " -0.093 2.00e-02 2.50e+03 pdb=" O GLU H 46 " 0.036 2.00e-02 2.50e+03 pdb=" N SER H 47 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 49 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLU H 49 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU H 49 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP H 50 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 11 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO H 12 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " -0.032 5.00e-02 4.00e+02 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 282 2.74 - 3.28: 3547 3.28 - 3.82: 5389 3.82 - 4.36: 6233 4.36 - 4.90: 11203 Nonbonded interactions: 26654 Sorted by model distance: nonbonded pdb=" O LEU c 8 " pdb=" OG1 THR c 18 " model vdw 2.196 3.040 nonbonded pdb=" O SER H 47 " pdb=" OG SER H 47 " model vdw 2.288 3.040 nonbonded pdb=" OG SER L 76 " pdb=" O ASP L 79 " model vdw 2.304 3.040 nonbonded pdb=" OG SER L 35 " pdb=" O ASN L 37 " model vdw 2.316 3.040 nonbonded pdb=" O SER C 95 " pdb=" OG SER C 95 " model vdw 2.319 3.040 ... (remaining 26649 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: 0.390 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.006 0.111 3653 Z= 0.295 Angle : 0.739 9.092 4971 Z= 0.415 Chirality : 0.047 0.317 574 Planarity : 0.006 0.057 641 Dihedral : 13.584 79.633 1305 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 0.50 % Allowed : 0.76 % Favored : 98.74 % 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: -2.56 (0.36), residues: 461 helix: -0.75 (0.74), residues: 47 sheet: -1.05 (0.40), residues: 177 loop : -2.45 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 47 TYR 0.013 0.001 TYR L 100 PHE 0.009 0.001 PHE L 80 TRP 0.029 0.004 TRP H 111 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 3652) covalent geometry : angle 0.73964 ( 4969) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.13353 ( 2) hydrogen bonds : bond 0.20598 ( 120) hydrogen bonds : angle 8.05504 ( 321) *********************** 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 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.087 Fit side-chains REVERT: c 2 LYS cc_start: 0.8156 (tttp) cc_final: 0.7924 (tttp) REVERT: c 53 SER cc_start: 0.8211 (t) cc_final: 0.7995 (t) outliers start: 2 outliers final: 2 residues processed: 109 average time/residue: 0.0655 time to fit residues: 8.7492 Evaluate side-chains 100 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086642 restraints weight = 4851.252| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.08 r_work: 0.3000 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3653 Z= 0.230 Angle : 0.693 6.828 4971 Z= 0.366 Chirality : 0.047 0.151 574 Planarity : 0.005 0.052 641 Dihedral : 5.249 37.666 506 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % 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: -2.74 (0.36), residues: 461 helix: -1.14 (0.72), residues: 48 sheet: -1.24 (0.38), residues: 185 loop : -2.47 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 47 TYR 0.013 0.002 TYR L 58 PHE 0.014 0.002 PHE C 94 TRP 0.022 0.002 TRP H 111 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3652) covalent geometry : angle 0.69300 ( 4969) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.08743 ( 2) hydrogen bonds : bond 0.04171 ( 120) hydrogen bonds : angle 6.17053 ( 321) *********************** 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 113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.097 Fit side-chains REVERT: L 90 GLU cc_start: 0.7562 (tp30) cc_final: 0.7286 (tp30) REVERT: H 14 LEU cc_start: 0.7581 (tp) cc_final: 0.7316 (tp) REVERT: H 26 LYS cc_start: 0.7514 (tptt) cc_final: 0.7258 (tppt) REVERT: H 49 GLU cc_start: 0.8235 (pm20) cc_final: 0.7655 (pm20) REVERT: c 53 SER cc_start: 0.8384 (t) cc_final: 0.8139 (t) outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 0.0707 time to fit residues: 9.1415 Evaluate side-chains 102 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain c residue 11 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084671 restraints weight = 4715.352| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.06 r_work: 0.2925 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 3653 Z= 0.333 Angle : 0.771 7.851 4971 Z= 0.407 Chirality : 0.050 0.155 574 Planarity : 0.005 0.052 641 Dihedral : 5.311 21.325 501 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.54 % Favored : 90.24 % Rotamer: Outliers : 6.55 % Allowed : 17.38 % 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 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: -2.93 (0.36), residues: 461 helix: -1.50 (0.72), residues: 48 sheet: -1.50 (0.37), residues: 191 loop : -2.41 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 47 TYR 0.015 0.002 TYR L 58 PHE 0.015 0.002 PHE C 94 TRP 0.016 0.002 TRP H 111 HIS 0.004 0.002 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00787 ( 3652) covalent geometry : angle 0.77108 ( 4969) SS BOND : bond 0.00328 ( 1) SS BOND : angle 0.26440 ( 2) hydrogen bonds : bond 0.04536 ( 120) hydrogen bonds : angle 6.05472 ( 321) *********************** 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 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.138 Fit side-chains REVERT: H 14 LEU cc_start: 0.7577 (tp) cc_final: 0.7316 (tp) REVERT: C 21 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7963 (pp) REVERT: c 53 SER cc_start: 0.8186 (t) cc_final: 0.7922 (t) REVERT: c 93 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8117 (p) outliers start: 26 outliers final: 19 residues processed: 115 average time/residue: 0.0677 time to fit residues: 9.5256 Evaluate side-chains 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 69 GLN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN L 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.088924 restraints weight = 4572.286| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.07 r_work: 0.2995 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3653 Z= 0.142 Angle : 0.645 7.075 4971 Z= 0.335 Chirality : 0.045 0.149 574 Planarity : 0.004 0.046 641 Dihedral : 4.785 19.930 501 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 4.28 % Allowed : 19.90 % Favored : 75.82 % 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: -2.70 (0.36), residues: 461 helix: -1.18 (0.74), residues: 48 sheet: -1.20 (0.38), residues: 185 loop : -2.44 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.013 0.001 TYR H 97 PHE 0.009 0.001 PHE L 106 TRP 0.010 0.001 TRP L 59 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3652) covalent geometry : angle 0.64476 ( 4969) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.09328 ( 2) hydrogen bonds : bond 0.03484 ( 120) hydrogen bonds : angle 5.59175 ( 321) *********************** 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 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.129 Fit side-chains REVERT: L 51 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: H 14 LEU cc_start: 0.7494 (tp) cc_final: 0.7192 (tp) REVERT: H 49 GLU cc_start: 0.8041 (pm20) cc_final: 0.7386 (pm20) REVERT: C 21 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7905 (pp) REVERT: c 18 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8655 (t) REVERT: c 53 SER cc_start: 0.8164 (t) cc_final: 0.7906 (t) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.0672 time to fit residues: 9.2699 Evaluate side-chains 109 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.124538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.089298 restraints weight = 4745.759| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.10 r_work: 0.3049 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3653 Z= 0.118 Angle : 0.614 6.398 4971 Z= 0.319 Chirality : 0.044 0.140 574 Planarity : 0.004 0.043 641 Dihedral : 4.505 19.347 501 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 4.28 % Allowed : 21.41 % Favored : 74.31 % 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: -2.52 (0.36), residues: 461 helix: -0.88 (0.74), residues: 48 sheet: -1.02 (0.38), residues: 185 loop : -2.41 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 47 TYR 0.008 0.001 TYR L 58 PHE 0.008 0.001 PHE L 106 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3652) covalent geometry : angle 0.61384 ( 4969) SS BOND : bond 0.00328 ( 1) SS BOND : angle 0.18595 ( 2) hydrogen bonds : bond 0.03122 ( 120) hydrogen bonds : angle 5.24933 ( 321) *********************** 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 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.085 Fit side-chains REVERT: L 90 GLU cc_start: 0.7904 (tp30) cc_final: 0.7687 (tm-30) REVERT: C 21 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8291 (pp) REVERT: c 18 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8474 (t) REVERT: c 53 SER cc_start: 0.8333 (t) cc_final: 0.8113 (t) REVERT: c 60 LYS cc_start: 0.7287 (tppt) cc_final: 0.7033 (tppt) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.0680 time to fit residues: 8.9242 Evaluate side-chains 106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.087858 restraints weight = 4604.268| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.12 r_work: 0.2982 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3653 Z= 0.185 Angle : 0.648 7.101 4971 Z= 0.339 Chirality : 0.045 0.137 574 Planarity : 0.004 0.042 641 Dihedral : 4.671 19.497 501 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.24 % Favored : 91.54 % Rotamer: Outliers : 5.29 % Allowed : 20.65 % Favored : 74.06 % 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: -2.50 (0.37), residues: 461 helix: -1.04 (0.73), residues: 48 sheet: -1.12 (0.37), residues: 202 loop : -2.31 (0.37), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 47 TYR 0.020 0.002 TYR H 30 PHE 0.009 0.001 PHE L 106 TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3652) covalent geometry : angle 0.64768 ( 4969) SS BOND : bond 0.00286 ( 1) SS BOND : angle 0.04625 ( 2) hydrogen bonds : bond 0.03480 ( 120) hydrogen bonds : angle 5.26804 ( 321) *********************** 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 120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.117 Fit side-chains REVERT: L 90 GLU cc_start: 0.8038 (tp30) cc_final: 0.7761 (tm-30) REVERT: H 49 GLU cc_start: 0.8084 (pm20) cc_final: 0.7609 (pm20) REVERT: C 21 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7984 (pp) REVERT: c 18 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8675 (t) REVERT: c 53 SER cc_start: 0.8215 (t) cc_final: 0.7958 (t) REVERT: c 60 LYS cc_start: 0.7244 (tppt) cc_final: 0.6901 (tppt) REVERT: c 93 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (p) REVERT: c 127 GLN cc_start: 0.9026 (mp10) cc_final: 0.8577 (mp10) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.0544 time to fit residues: 7.5325 Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.0770 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088016 restraints weight = 4858.324| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.13 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3653 Z= 0.138 Angle : 0.622 6.540 4971 Z= 0.323 Chirality : 0.044 0.131 574 Planarity : 0.004 0.041 641 Dihedral : 4.494 18.955 501 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.41 % Rotamer: Outliers : 5.29 % Allowed : 20.91 % Favored : 73.80 % 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: -2.43 (0.37), residues: 461 helix: -0.97 (0.73), residues: 49 sheet: -1.08 (0.37), residues: 202 loop : -2.26 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 47 TYR 0.021 0.001 TYR H 30 PHE 0.007 0.001 PHE L 106 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3652) covalent geometry : angle 0.62217 ( 4969) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.12702 ( 2) hydrogen bonds : bond 0.03159 ( 120) hydrogen bonds : angle 5.12625 ( 321) *********************** 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 119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.088 Fit side-chains REVERT: L 51 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: H 49 GLU cc_start: 0.8243 (pm20) cc_final: 0.7990 (pm20) REVERT: C 21 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8309 (pp) REVERT: c 18 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (t) REVERT: c 53 SER cc_start: 0.8348 (t) cc_final: 0.8110 (t) REVERT: c 60 LYS cc_start: 0.7194 (tppt) cc_final: 0.6918 (tppt) REVERT: c 93 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7980 (p) REVERT: c 127 GLN cc_start: 0.9125 (mp10) cc_final: 0.8825 (mp10) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.0613 time to fit residues: 8.4190 Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 0.0170 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088187 restraints weight = 4832.264| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.12 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 3653 Z= 0.146 Angle : 0.636 6.771 4971 Z= 0.330 Chirality : 0.044 0.129 574 Planarity : 0.004 0.041 641 Dihedral : 4.493 18.964 501 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 6.05 % Allowed : 20.91 % Favored : 73.05 % 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: -2.39 (0.37), residues: 461 helix: -0.94 (0.72), residues: 49 sheet: -1.05 (0.37), residues: 199 loop : -2.22 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 47 TYR 0.019 0.001 TYR H 30 PHE 0.007 0.001 PHE L 106 TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3652) covalent geometry : angle 0.63564 ( 4969) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.06373 ( 2) hydrogen bonds : bond 0.03175 ( 120) hydrogen bonds : angle 5.07899 ( 321) *********************** 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 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.107 Fit side-chains REVERT: H 84 MET cc_start: 0.7790 (ptt) cc_final: 0.7375 (ptt) REVERT: C 21 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8336 (pp) REVERT: c 18 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8564 (t) REVERT: c 53 SER cc_start: 0.8334 (t) cc_final: 0.8099 (t) REVERT: c 60 LYS cc_start: 0.7267 (tppt) cc_final: 0.6932 (tppt) REVERT: c 93 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7981 (p) REVERT: c 127 GLN cc_start: 0.9110 (mp10) cc_final: 0.8843 (mp10) outliers start: 24 outliers final: 18 residues processed: 110 average time/residue: 0.0563 time to fit residues: 7.6974 Evaluate side-chains 114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 51 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095088 restraints weight = 4707.061| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.06 r_work: 0.3136 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 3653 Z= 0.110 Angle : 0.613 7.100 4971 Z= 0.315 Chirality : 0.043 0.136 574 Planarity : 0.004 0.039 641 Dihedral : 4.060 17.309 501 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.53 % Allowed : 23.93 % Favored : 72.54 % 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: -1.94 (0.37), residues: 461 helix: -0.22 (0.74), residues: 49 sheet: -0.59 (0.38), residues: 189 loop : -2.18 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.018 0.001 TYR H 30 PHE 0.006 0.001 PHE c 94 TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3652) covalent geometry : angle 0.61321 ( 4969) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.36590 ( 2) hydrogen bonds : bond 0.02616 ( 120) hydrogen bonds : angle 4.76984 ( 321) *********************** 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 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.143 Fit side-chains REVERT: L 51 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: H 113 GLN cc_start: 0.7395 (pm20) cc_final: 0.7145 (pm20) REVERT: C 21 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8245 (pp) REVERT: C 24 ARG cc_start: 0.8273 (ttm170) cc_final: 0.8049 (mmt90) REVERT: c 53 SER cc_start: 0.8297 (t) cc_final: 0.8092 (t) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.0602 time to fit residues: 8.3876 Evaluate side-chains 107 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 51 GLN L 98 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090565 restraints weight = 4836.423| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.06 r_work: 0.3068 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 3653 Z= 0.165 Angle : 0.677 7.978 4971 Z= 0.347 Chirality : 0.045 0.150 574 Planarity : 0.004 0.039 641 Dihedral : 4.439 19.146 501 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.53 % Allowed : 25.19 % Favored : 71.28 % 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: -2.09 (0.38), residues: 461 helix: -0.36 (0.75), residues: 49 sheet: -0.91 (0.37), residues: 200 loop : -2.07 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 47 TYR 0.019 0.001 TYR H 30 PHE 0.006 0.001 PHE L 106 TRP 0.023 0.002 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3652) covalent geometry : angle 0.67724 ( 4969) SS BOND : bond 0.00394 ( 1) SS BOND : angle 0.15304 ( 2) hydrogen bonds : bond 0.03087 ( 120) hydrogen bonds : angle 4.81874 ( 321) ********************** 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 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.138 Fit side-chains REVERT: L 98 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: C 21 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (pp) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.0588 time to fit residues: 7.6043 Evaluate side-chains 104 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 98 GLN Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 36 SER Chi-restraints excluded: chain c residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091235 restraints weight = 4709.998| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.03 r_work: 0.3073 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 3653 Z= 0.178 Angle : 0.735 13.189 4971 Z= 0.386 Chirality : 0.047 0.313 574 Planarity : 0.005 0.081 641 Dihedral : 4.446 18.858 501 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.53 % Allowed : 25.69 % Favored : 70.78 % 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: -1.97 (0.38), residues: 461 helix: -0.30 (0.74), residues: 49 sheet: -0.57 (0.39), residues: 184 loop : -2.20 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.019 0.002 TYR H 30 PHE 0.009 0.001 PHE L 101 TRP 0.019 0.002 TRP H 50 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3652) covalent geometry : angle 0.73513 ( 4969) SS BOND : bond 0.00364 ( 1) SS BOND : angle 0.23551 ( 2) hydrogen bonds : bond 0.03039 ( 120) hydrogen bonds : angle 4.78211 ( 321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 969.89 seconds wall clock time: 17 minutes 24.20 seconds (1044.20 seconds total)