Starting phenix.real_space_refine on Wed Mar 5 21:32:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5f_37290/03_2025/8w5f_37290.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.194 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 10 5.16 5 C 2326 2.51 5 N 637 2.21 5 O 727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3700 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 790 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "c" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 2.93, per 1000 atoms: 0.79 Number of scatterers: 3700 At special positions: 0 Unit cell: (88.4, 66.64, 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 10 16.00 O 727 8.00 N 637 7.00 C 2326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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: 0.95 Conformation dependent library (CDL) restraints added in 480.5 milliseconds 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 10.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'c' and resid 101 through 116 removed outlier: 3.645A pdb=" N ARG c 109 " --> pdb=" O ARG c 105 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR c 110 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing helix chain 'c' and resid 118 through 127 removed outlier: 3.630A pdb=" N GLN c 127 " --> pdb=" O ASP c 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.613A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 removed outlier: 4.037A pdb=" N ASP C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.514A pdb=" N VAL L 37 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR L 89 " --> pdb=" O CYS L 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.837A pdb=" N GLU H 29 " --> pdb=" O THR H 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.542A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 6 through 11 removed outlier: 6.180A pdb=" N GLN c 17 " --> pdb=" O ASN c 10 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS c 74 " --> pdb=" O VAL c 84 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL c 84 " --> pdb=" O CYS c 74 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLN c 87 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR C 97 " --> pdb=" O GLN c 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP c 91 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 62 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 47 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 327 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: 1.01 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1211 1.34 - 1.46: 773 1.46 - 1.58: 1779 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3775 Sorted by residual: bond pdb=" C SER L 25 " pdb=" N PRO L 26 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" CB PRO c 28 " pdb=" CG PRO c 28 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.34e+00 bond pdb=" CA GLU H 108 " pdb=" CB GLU H 108 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.30e-02 5.92e+03 8.58e-01 bond pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.41e-02 5.03e+03 8.39e-01 bond pdb=" N PRO H 26 " pdb=" CA PRO H 26 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.11e-01 ... (remaining 3770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 5054 2.77 - 5.55: 73 5.55 - 8.32: 9 8.32 - 11.09: 1 11.09 - 13.86: 1 Bond angle restraints: 5138 Sorted by residual: angle pdb=" C VAL H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta sigma weight residual 121.80 135.66 -13.86 2.44e+00 1.68e-01 3.23e+01 angle pdb=" C SER L 30 " pdb=" N VAL L 31 " pdb=" CA VAL L 31 " ideal model delta sigma weight residual 121.97 128.98 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" C SER L 98 " pdb=" N GLU L 99 " pdb=" CA GLU L 99 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N PRO H 26 " pdb=" CA PRO H 26 " pdb=" C PRO H 26 " ideal model delta sigma weight residual 112.47 120.34 -7.87 2.06e+00 2.36e-01 1.46e+01 angle pdb=" C GLY c 12 " pdb=" N LYS c 13 " pdb=" CA LYS c 13 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 5133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 1998 15.75 - 31.50: 216 31.50 - 47.25: 35 47.25 - 63.00: 8 63.00 - 78.75: 3 Dihedral angle restraints: 2260 sinusoidal: 858 harmonic: 1402 Sorted by residual: dihedral pdb=" CA SER L 25 " pdb=" C SER L 25 " pdb=" N PRO L 26 " pdb=" CA PRO L 26 " ideal model delta harmonic sigma weight residual -180.00 -137.47 -42.53 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA ILE c 11 " pdb=" C ILE c 11 " pdb=" N GLY c 12 " pdb=" CA GLY c 12 " ideal model delta harmonic sigma weight residual 180.00 -138.43 -41.57 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA TRP L 114 " pdb=" C TRP L 114 " pdb=" N THR L 115 " pdb=" CA THR L 115 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 2257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 454 0.052 - 0.103: 102 0.103 - 0.154: 30 0.154 - 0.206: 1 0.206 - 0.257: 1 Chirality restraints: 588 Sorted by residual: chirality pdb=" CA PRO H 26 " pdb=" N PRO H 26 " pdb=" C PRO H 26 " pdb=" CB PRO H 26 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN H 74 " pdb=" N ASN H 74 " pdb=" C ASN H 74 " pdb=" CB ASN H 74 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA THR L 112 " pdb=" N THR L 112 " pdb=" C THR L 112 " pdb=" CB THR L 112 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 585 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 25 " 0.065 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO H 26 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 26 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO H 26 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 25 " -0.059 5.00e-02 4.00e+02 9.03e-02 1.30e+01 pdb=" N PRO L 26 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO L 26 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 26 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 25 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C GLN H 25 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN H 25 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO H 26 " 0.013 2.00e-02 2.50e+03 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1130 2.82 - 3.34: 3163 3.34 - 3.86: 5529 3.86 - 4.38: 6386 4.38 - 4.90: 11858 Nonbonded interactions: 28066 Sorted by model distance: nonbonded pdb=" NZ LYS H 86 " pdb=" O SER H 104 " model vdw 2.296 3.120 nonbonded pdb=" NH1 ARG L 79 " pdb=" OD2 ASP L 100 " model vdw 2.303 3.120 nonbonded pdb=" N THR H 106 " pdb=" OD2 ASP H 109 " model vdw 2.333 3.120 nonbonded pdb=" O ASN C 70 " pdb=" ND2 ASN C 70 " model vdw 2.335 3.120 nonbonded pdb=" OE2 GLU H 65 " pdb=" NZ LYS H 82 " model vdw 2.371 3.120 ... (remaining 28061 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' } 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: 0.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3775 Z= 0.254 Angle : 0.822 13.864 5138 Z= 0.433 Chirality : 0.048 0.257 588 Planarity : 0.007 0.100 665 Dihedral : 13.392 78.749 1356 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.85 % Favored : 88.68 % Rotamer: Outliers : 0.25 % Allowed : 0.49 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.36), residues: 477 helix: -1.02 (0.75), residues: 44 sheet: -1.42 (0.38), residues: 190 loop : -2.68 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 132 HIS 0.003 0.001 HIS L 55 PHE 0.008 0.001 PHE L 116 TYR 0.012 0.001 TYR L 54 ARG 0.003 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.446 Fit side-chains REVERT: L 54 TYR cc_start: 0.9216 (m-80) cc_final: 0.8931 (m-80) REVERT: C 27 ASN cc_start: 0.8485 (t0) cc_final: 0.8012 (t0) REVERT: C 30 ASN cc_start: 0.9021 (p0) cc_final: 0.8619 (p0) REVERT: C 60 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8020 (pttp) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.1846 time to fit residues: 20.6484 Evaluate side-chains 93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097998 restraints weight = 4961.942| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.30 r_work: 0.3005 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3775 Z= 0.226 Angle : 0.765 11.202 5138 Z= 0.394 Chirality : 0.048 0.242 588 Planarity : 0.006 0.084 665 Dihedral : 5.987 38.439 525 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.85 % Favored : 88.68 % Rotamer: Outliers : 1.23 % Allowed : 10.12 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.37), residues: 477 helix: -0.34 (0.76), residues: 46 sheet: -1.13 (0.39), residues: 190 loop : -2.66 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS L 55 PHE 0.008 0.001 PHE L 116 TYR 0.010 0.001 TYR L 48 ARG 0.003 0.001 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.418 Fit side-chains REVERT: L 92 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8585 (ttpt) REVERT: H 65 GLU cc_start: 0.8947 (tp30) cc_final: 0.8731 (tp30) REVERT: H 109 ASP cc_start: 0.7902 (m-30) cc_final: 0.7564 (m-30) REVERT: C 27 ASN cc_start: 0.8729 (t0) cc_final: 0.8260 (t0) REVERT: C 30 ASN cc_start: 0.9103 (p0) cc_final: 0.8650 (p0) REVERT: C 60 LYS cc_start: 0.8831 (mtmt) cc_final: 0.7526 (pttp) REVERT: C 70 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.9027 (p0) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1627 time to fit residues: 21.1168 Evaluate side-chains 103 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.0010 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 87 GLN C 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098111 restraints weight = 4953.920| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.31 r_work: 0.3003 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3775 Z= 0.214 Angle : 0.743 10.069 5138 Z= 0.376 Chirality : 0.047 0.268 588 Planarity : 0.007 0.118 665 Dihedral : 5.712 35.763 525 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.47 % Allowed : 9.43 % Favored : 89.10 % Rotamer: Outliers : 3.21 % Allowed : 13.58 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.37), residues: 477 helix: 0.05 (0.79), residues: 46 sheet: -0.79 (0.39), residues: 187 loop : -2.49 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 132 HIS 0.002 0.001 HIS L 55 PHE 0.008 0.001 PHE L 116 TYR 0.010 0.001 TYR L 48 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.400 Fit side-chains REVERT: L 92 LYS cc_start: 0.9058 (ptmm) cc_final: 0.8554 (ttpt) REVERT: H 109 ASP cc_start: 0.7852 (m-30) cc_final: 0.7487 (m-30) REVERT: c 123 ASP cc_start: 0.8537 (m-30) cc_final: 0.8327 (m-30) REVERT: C 13 LYS cc_start: 0.8821 (tptt) cc_final: 0.8525 (tppt) REVERT: C 27 ASN cc_start: 0.8713 (t0) cc_final: 0.8279 (t0) REVERT: C 30 ASN cc_start: 0.9100 (p0) cc_final: 0.8682 (p0) REVERT: C 70 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8984 (p0) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1709 time to fit residues: 22.4482 Evaluate side-chains 111 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 121 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.0270 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 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 = 0.3490 r_free = 0.3490 target = 0.126075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.099391 restraints weight = 4926.229| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.31 r_work: 0.3025 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3775 Z= 0.187 Angle : 0.705 9.239 5138 Z= 0.359 Chirality : 0.046 0.247 588 Planarity : 0.006 0.094 665 Dihedral : 5.398 32.208 525 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.26 % Allowed : 8.81 % Favored : 89.94 % Rotamer: Outliers : 3.95 % Allowed : 14.57 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.38), residues: 477 helix: -0.14 (0.77), residues: 48 sheet: -0.62 (0.39), residues: 187 loop : -2.38 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.001 0.001 HIS L 55 PHE 0.008 0.001 PHE L 116 TYR 0.009 0.001 TYR L 48 ARG 0.003 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: L 45 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7152 (mp0) REVERT: H 65 GLU cc_start: 0.8861 (tp30) cc_final: 0.8634 (tp30) REVERT: H 86 LYS cc_start: 0.9035 (tppp) cc_final: 0.8825 (tptm) REVERT: H 109 ASP cc_start: 0.7875 (m-30) cc_final: 0.7474 (m-30) REVERT: C 13 LYS cc_start: 0.8765 (tptt) cc_final: 0.8461 (tppt) REVERT: C 27 ASN cc_start: 0.8684 (t0) cc_final: 0.8260 (t0) REVERT: C 30 ASN cc_start: 0.9104 (p0) cc_final: 0.8723 (p0) REVERT: C 45 GLU cc_start: 0.8594 (pt0) cc_final: 0.8389 (pt0) REVERT: C 70 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (p0) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 0.1696 time to fit residues: 24.4855 Evaluate side-chains 113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.093002 restraints weight = 5140.446| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.28 r_work: 0.2922 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3775 Z= 0.371 Angle : 0.805 9.522 5138 Z= 0.414 Chirality : 0.051 0.238 588 Planarity : 0.006 0.086 665 Dihedral : 5.935 39.995 525 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.95 % Favored : 87.00 % Rotamer: Outliers : 4.44 % Allowed : 17.04 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.38), residues: 477 helix: -0.23 (0.76), residues: 50 sheet: -0.72 (0.39), residues: 187 loop : -2.42 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 132 HIS 0.003 0.001 HIS L 55 PHE 0.012 0.002 PHE c 94 TYR 0.012 0.002 TYR c 89 ARG 0.005 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.428 Fit side-chains REVERT: L 25 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7510 (p) REVERT: L 92 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8638 (ttpt) REVERT: H 65 GLU cc_start: 0.8942 (tp30) cc_final: 0.8717 (tp30) REVERT: H 109 ASP cc_start: 0.7946 (m-30) cc_final: 0.7485 (m-30) REVERT: c 127 GLN cc_start: 0.9009 (mp10) cc_final: 0.8558 (mp10) REVERT: C 13 LYS cc_start: 0.8808 (tptt) cc_final: 0.8534 (tppt) REVERT: C 27 ASN cc_start: 0.8726 (t0) cc_final: 0.8278 (t0) REVERT: C 30 ASN cc_start: 0.9124 (p0) cc_final: 0.8697 (p0) REVERT: C 45 GLU cc_start: 0.8646 (pt0) cc_final: 0.8377 (pt0) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.1581 time to fit residues: 20.4373 Evaluate side-chains 111 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097591 restraints weight = 5013.383| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.31 r_work: 0.3009 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3775 Z= 0.194 Angle : 0.711 8.450 5138 Z= 0.363 Chirality : 0.046 0.242 588 Planarity : 0.005 0.079 665 Dihedral : 5.411 34.162 523 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 1.05 % Allowed : 8.39 % Favored : 90.57 % Rotamer: Outliers : 4.69 % Allowed : 17.78 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.38), residues: 477 helix: -0.13 (0.75), residues: 50 sheet: -0.43 (0.41), residues: 179 loop : -2.39 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.001 0.001 HIS L 55 PHE 0.007 0.001 PHE L 80 TYR 0.010 0.001 TYR L 48 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.384 Fit side-chains REVERT: L 92 LYS cc_start: 0.9015 (ptmm) cc_final: 0.8523 (ttpt) REVERT: L 97 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: H 86 LYS cc_start: 0.8996 (tppp) cc_final: 0.8689 (tptm) REVERT: H 109 ASP cc_start: 0.7908 (m-30) cc_final: 0.7459 (m-30) REVERT: c 123 ASP cc_start: 0.8434 (m-30) cc_final: 0.8233 (m-30) REVERT: C 27 ASN cc_start: 0.8679 (t0) cc_final: 0.8258 (t0) REVERT: C 30 ASN cc_start: 0.9069 (p0) cc_final: 0.8689 (p0) REVERT: C 45 GLU cc_start: 0.8671 (pt0) cc_final: 0.8415 (pt0) REVERT: C 70 ASN cc_start: 0.9215 (p0) cc_final: 0.8908 (p0) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.1716 time to fit residues: 23.1283 Evaluate side-chains 113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.0770 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 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 = 0.3527 r_free = 0.3527 target = 0.129064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102370 restraints weight = 4948.034| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.29 r_work: 0.3077 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3775 Z= 0.164 Angle : 0.685 9.291 5138 Z= 0.349 Chirality : 0.045 0.239 588 Planarity : 0.005 0.076 665 Dihedral : 4.979 28.083 523 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.22 % Favored : 89.94 % Rotamer: Outliers : 4.20 % Allowed : 18.52 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.39), residues: 477 helix: 0.19 (0.75), residues: 50 sheet: -0.28 (0.40), residues: 186 loop : -2.21 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.001 0.000 HIS H 54 PHE 0.008 0.001 PHE L 116 TYR 0.015 0.001 TYR H 122 ARG 0.001 0.000 ARG L 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.415 Fit side-chains REVERT: L 45 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6974 (mp0) REVERT: L 92 LYS cc_start: 0.8998 (ptmm) cc_final: 0.8595 (ttpt) REVERT: H 86 LYS cc_start: 0.9005 (tppp) cc_final: 0.8561 (tptm) REVERT: H 109 ASP cc_start: 0.7834 (m-30) cc_final: 0.7282 (m-30) REVERT: c 16 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8301 (mtmt) REVERT: c 63 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8400 (mttm) REVERT: c 123 ASP cc_start: 0.8433 (m-30) cc_final: 0.8186 (m-30) REVERT: C 27 ASN cc_start: 0.8619 (t0) cc_final: 0.8227 (t0) REVERT: C 30 ASN cc_start: 0.8961 (p0) cc_final: 0.8694 (p0) REVERT: C 45 GLU cc_start: 0.8592 (pt0) cc_final: 0.8338 (pt0) REVERT: C 70 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8669 (p0) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.1654 time to fit residues: 24.7216 Evaluate side-chains 114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 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 = 0.3470 r_free = 0.3470 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.097454 restraints weight = 5078.246| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.30 r_work: 0.3004 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3775 Z= 0.238 Angle : 0.729 8.803 5138 Z= 0.376 Chirality : 0.049 0.233 588 Planarity : 0.005 0.075 665 Dihedral : 5.221 33.445 523 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.27 % Favored : 88.89 % Rotamer: Outliers : 4.20 % Allowed : 19.75 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.39), residues: 477 helix: 0.13 (0.75), residues: 50 sheet: -0.17 (0.40), residues: 184 loop : -2.15 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.003 0.001 HIS H 54 PHE 0.009 0.001 PHE c 94 TYR 0.016 0.002 TYR H 131 ARG 0.003 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.434 Fit side-chains REVERT: L 45 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7013 (mp0) REVERT: L 92 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8530 (ttpt) REVERT: H 86 LYS cc_start: 0.9027 (tppp) cc_final: 0.8676 (tptm) REVERT: H 109 ASP cc_start: 0.7882 (m-30) cc_final: 0.7377 (m-30) REVERT: c 16 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8474 (mtmm) REVERT: C 27 ASN cc_start: 0.8621 (t0) cc_final: 0.8207 (t0) REVERT: C 30 ASN cc_start: 0.9054 (p0) cc_final: 0.8672 (p0) REVERT: C 70 ASN cc_start: 0.9278 (p0) cc_final: 0.8981 (p0) outliers start: 17 outliers final: 16 residues processed: 107 average time/residue: 0.1821 time to fit residues: 23.3410 Evaluate side-chains 113 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099391 restraints weight = 4933.327| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.26 r_work: 0.3032 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3775 Z= 0.191 Angle : 0.709 9.647 5138 Z= 0.363 Chirality : 0.047 0.235 588 Planarity : 0.005 0.073 665 Dihedral : 5.122 31.555 523 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.22 % Favored : 89.94 % Rotamer: Outliers : 4.44 % Allowed : 20.49 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.39), residues: 477 helix: 0.17 (0.75), residues: 50 sheet: 0.00 (0.41), residues: 176 loop : -2.06 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 132 HIS 0.003 0.001 HIS H 54 PHE 0.006 0.001 PHE L 116 TYR 0.016 0.001 TYR H 122 ARG 0.009 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.451 Fit side-chains REVERT: L 45 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6996 (mp0) REVERT: L 92 LYS cc_start: 0.9018 (ptmm) cc_final: 0.8526 (ttpt) REVERT: H 86 LYS cc_start: 0.8984 (tppp) cc_final: 0.8693 (tptm) REVERT: H 109 ASP cc_start: 0.7904 (m-30) cc_final: 0.7396 (m-30) REVERT: c 16 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8381 (mtmt) REVERT: c 63 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8391 (mttm) REVERT: C 27 ASN cc_start: 0.8603 (t0) cc_final: 0.8197 (t0) REVERT: C 30 ASN cc_start: 0.8989 (p0) cc_final: 0.8684 (p0) REVERT: C 70 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8815 (p0) outliers start: 18 outliers final: 16 residues processed: 105 average time/residue: 0.1812 time to fit residues: 22.7798 Evaluate side-chains 115 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 25 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 = 0.3475 r_free = 0.3475 target = 0.124343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098012 restraints weight = 4926.419| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.24 r_work: 0.3015 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3775 Z= 0.217 Angle : 0.723 9.546 5138 Z= 0.370 Chirality : 0.048 0.233 588 Planarity : 0.005 0.072 665 Dihedral : 5.212 33.278 523 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.06 % Favored : 89.10 % Rotamer: Outliers : 5.19 % Allowed : 19.75 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.39), residues: 477 helix: 0.15 (0.75), residues: 50 sheet: -0.01 (0.41), residues: 176 loop : -2.05 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 132 HIS 0.002 0.001 HIS H 54 PHE 0.009 0.001 PHE c 94 TYR 0.017 0.002 TYR H 122 ARG 0.008 0.001 ARG L 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.482 Fit side-chains REVERT: L 45 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7002 (mp0) REVERT: L 92 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8533 (ttpt) REVERT: H 86 LYS cc_start: 0.9018 (tppp) cc_final: 0.8689 (tptm) REVERT: H 109 ASP cc_start: 0.7929 (m-30) cc_final: 0.7446 (m-30) REVERT: c 16 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8417 (mtmt) REVERT: c 63 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8380 (mttm) REVERT: C 27 ASN cc_start: 0.8631 (t0) cc_final: 0.8214 (t0) REVERT: C 30 ASN cc_start: 0.9036 (p0) cc_final: 0.8667 (p0) REVERT: C 70 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8975 (p0) outliers start: 21 outliers final: 19 residues processed: 104 average time/residue: 0.1989 time to fit residues: 25.5410 Evaluate side-chains 114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain c residue 11 ILE Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 80 CYS Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.120070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093665 restraints weight = 5114.759| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.27 r_work: 0.2952 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3775 Z= 0.336 Angle : 0.795 9.620 5138 Z= 0.408 Chirality : 0.051 0.229 588 Planarity : 0.006 0.073 665 Dihedral : 5.706 39.132 523 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.90 % Favored : 88.26 % Rotamer: Outliers : 4.94 % Allowed : 20.49 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.39), residues: 477 helix: 0.01 (0.76), residues: 50 sheet: -0.16 (0.41), residues: 177 loop : -2.13 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 132 HIS 0.003 0.001 HIS L 55 PHE 0.012 0.002 PHE c 94 TYR 0.016 0.002 TYR H 122 ARG 0.008 0.001 ARG L 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.62 seconds wall clock time: 38 minutes 24.22 seconds (2304.22 seconds total)