Starting phenix.real_space_refine on Wed Mar 5 21:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8i_24237/03_2025/7n8i_24237.cif" } resolution = 3.0 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= 0.000 sd= 0.053 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 13 5.16 5 C 2315 2.51 5 N 581 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 3600 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1759 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.89, per 1000 atoms: 1.64 Number of scatterers: 3600 At special positions: 0 Unit cell: (56.481, 85.143, 75.87, 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 13 16.00 O 691 8.00 N 581 7.00 C 2315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 282 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 464.0 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 9 sheets defined 5.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.867A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.910A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.381A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.609A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.625A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.944A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.090A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 369 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: 1.17 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 593 1.31 - 1.44: 1076 1.44 - 1.57: 1999 1.57 - 1.69: 6 1.69 - 1.82: 17 Bond restraints: 3691 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.89e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.45e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.585 -0.055 2.00e-02 2.50e+03 7.43e+00 ... (remaining 3686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4350 1.62 - 3.24: 543 3.24 - 4.86: 69 4.86 - 6.48: 38 6.48 - 8.10: 11 Bond angle restraints: 5011 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.12 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.42 -8.10 1.14e+00 7.69e-01 5.05e+01 angle pdb=" C TYR A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.01e+00 9.80e-01 4.49e+01 angle pdb=" C LEU A 216 " pdb=" N PRO A 217 " pdb=" CA PRO A 217 " ideal model delta sigma weight residual 119.85 126.54 -6.69 1.01e+00 9.80e-01 4.39e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.55 -6.79 1.03e+00 9.43e-01 4.35e+01 ... (remaining 5006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 2112 16.43 - 32.86: 78 32.86 - 49.29: 13 49.29 - 65.72: 10 65.72 - 82.14: 4 Dihedral angle restraints: 2217 sinusoidal: 925 harmonic: 1292 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.69 40.31 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " pdb=" CG ASN A 165 " pdb=" OD1 ASN A 165 " ideal model delta sinusoidal sigma weight residual 120.00 -168.17 -71.83 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 2214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 397 0.064 - 0.127: 121 0.127 - 0.190: 27 0.190 - 0.254: 10 0.254 - 0.317: 6 Chirality restraints: 561 Sorted by residual: chirality pdb=" C2 NAG A1303 " pdb=" C1 NAG A1303 " pdb=" C3 NAG A1303 " pdb=" N2 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C2 NAG A1305 " pdb=" C1 NAG A1305 " pdb=" C3 NAG A1305 " pdb=" N2 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 558 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.026 2.00e-02 2.50e+03 2.66e-02 8.86e+00 pdb=" CG ASN A 165 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 28 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C ASP L 28 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP L 28 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE L 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 7 " -0.014 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C SER L 7 " 0.046 2.00e-02 2.50e+03 pdb=" O SER L 7 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO L 8 " -0.015 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1070 2.83 - 3.35: 2861 3.35 - 3.86: 5945 3.86 - 4.38: 7279 4.38 - 4.90: 12391 Nonbonded interactions: 29546 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.532 3.120 nonbonded pdb=" N ASP H 54 " pdb=" N GLY H 55 " model vdw 2.566 2.560 nonbonded pdb=" OD1 ASN A 165 " pdb=" O5 NAG A1304 " model vdw 2.597 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" N THR A 109 " model vdw 2.610 3.120 ... (remaining 29541 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 11.620 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.740 Find NCS groups from input model: 0.040 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:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.011 0.057 3691 Z= 0.694 Angle : 1.232 8.102 5011 Z= 0.830 Chirality : 0.074 0.317 561 Planarity : 0.006 0.029 631 Dihedral : 10.639 82.143 1379 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.40), residues: 431 helix: -1.13 (1.30), residues: 17 sheet: 1.05 (0.35), residues: 206 loop : 0.62 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP A 64 HIS 0.002 0.001 HIS A 66 PHE 0.015 0.003 PHE A 55 TYR 0.028 0.004 TYR H 104 ARG 0.003 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.413 Fit side-chains REVERT: L 30 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8047 (mtm180) REVERT: L 81 GLU cc_start: 0.7524 (pm20) cc_final: 0.7197 (pm20) REVERT: H 34 MET cc_start: 0.9008 (mmm) cc_final: 0.8508 (mmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.9955 time to fit residues: 82.5354 Evaluate side-chains 52 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 chunk 39 optimal weight: 0.1980 overall best weight: 0.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101126 restraints weight = 4151.012| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.31 r_work: 0.2907 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3691 Z= 0.136 Angle : 0.505 4.944 5011 Z= 0.267 Chirality : 0.044 0.167 561 Planarity : 0.004 0.033 631 Dihedral : 4.628 35.376 588 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.80 % Allowed : 9.02 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.51 (0.41), residues: 431 helix: 3.07 (1.67), residues: 11 sheet: 1.31 (0.35), residues: 203 loop : 0.71 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 PHE 0.009 0.001 PHE A 55 TYR 0.012 0.001 TYR A 170 ARG 0.004 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.426 Fit side-chains REVERT: L 30 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.7962 (mtm180) REVERT: L 42 LYS cc_start: 0.8666 (mptt) cc_final: 0.8310 (mmtm) REVERT: L 81 GLU cc_start: 0.8094 (pm20) cc_final: 0.7654 (pm20) REVERT: H 13 GLN cc_start: 0.8331 (mm110) cc_final: 0.8070 (mm-40) REVERT: H 89 GLU cc_start: 0.8505 (pt0) cc_final: 0.7996 (mp0) REVERT: A 129 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8538 (mtmt) REVERT: A 206 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8719 (ttmt) REVERT: A 304 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8267 (mttt) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 1.1548 time to fit residues: 81.3770 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 42 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.093420 restraints weight = 4154.611| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.36 r_work: 0.2802 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3691 Z= 0.289 Angle : 0.585 8.125 5011 Z= 0.299 Chirality : 0.047 0.175 561 Planarity : 0.004 0.033 631 Dihedral : 5.516 49.561 588 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 7.99 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.41), residues: 431 helix: 0.39 (1.53), residues: 17 sheet: 1.33 (0.35), residues: 207 loop : 0.59 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS A 49 PHE 0.013 0.002 PHE A 133 TYR 0.012 0.002 TYR A 279 ARG 0.003 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.378 Fit side-chains REVERT: L 30 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.7869 (mtm180) REVERT: H 17 SER cc_start: 0.8918 (p) cc_final: 0.8689 (m) REVERT: H 89 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 41 LYS cc_start: 0.7033 (mmpt) cc_final: 0.4958 (tmtt) REVERT: A 129 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8481 (mtmt) REVERT: A 287 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8482 (t0) outliers start: 11 outliers final: 4 residues processed: 63 average time/residue: 1.2015 time to fit residues: 78.2380 Evaluate side-chains 58 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 0.4980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.106963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090298 restraints weight = 4300.664| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.46 r_work: 0.2758 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3691 Z= 0.273 Angle : 0.563 9.097 5011 Z= 0.282 Chirality : 0.046 0.170 561 Planarity : 0.004 0.034 631 Dihedral : 5.247 41.298 588 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.84 % Allowed : 9.02 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.37 (0.41), residues: 431 helix: 3.45 (1.76), residues: 11 sheet: 1.38 (0.35), residues: 204 loop : 0.38 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.002 PHE A 133 TYR 0.011 0.001 TYR A 279 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.412 Fit side-chains REVERT: L 30 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.7821 (mtm180) REVERT: L 103 LYS cc_start: 0.8706 (tttt) cc_final: 0.8127 (tptp) REVERT: H 17 SER cc_start: 0.8898 (p) cc_final: 0.8669 (m) REVERT: H 89 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: A 129 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8444 (mtmt) REVERT: A 205 SER cc_start: 0.9145 (p) cc_final: 0.8920 (t) REVERT: A 287 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (t0) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 1.1838 time to fit residues: 79.5103 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.089446 restraints weight = 4345.452| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.48 r_work: 0.2756 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3691 Z= 0.271 Angle : 0.561 7.877 5011 Z= 0.284 Chirality : 0.046 0.174 561 Planarity : 0.004 0.035 631 Dihedral : 5.764 49.990 588 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 10.05 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.39 (0.42), residues: 431 helix: 3.52 (1.77), residues: 11 sheet: 1.48 (0.36), residues: 199 loop : 0.33 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.002 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.380 Fit side-chains REVERT: L 30 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.7802 (mtm180) REVERT: L 103 LYS cc_start: 0.8715 (tttt) cc_final: 0.8114 (tptp) REVERT: H 17 SER cc_start: 0.8875 (p) cc_final: 0.8662 (m) REVERT: H 89 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 129 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8453 (mtmt) REVERT: A 205 SER cc_start: 0.9143 (p) cc_final: 0.8929 (t) REVERT: A 287 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8438 (t0) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 1.2835 time to fit residues: 81.9823 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.090288 restraints weight = 4278.408| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.46 r_work: 0.2750 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3691 Z= 0.250 Angle : 0.546 8.474 5011 Z= 0.275 Chirality : 0.046 0.161 561 Planarity : 0.004 0.035 631 Dihedral : 6.164 59.863 588 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.58 % Allowed : 10.31 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.41), residues: 431 helix: 3.53 (1.77), residues: 11 sheet: 1.45 (0.36), residues: 204 loop : 0.20 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.001 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.378 Fit side-chains REVERT: L 30 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.7803 (mtm180) REVERT: L 42 LYS cc_start: 0.8858 (mptt) cc_final: 0.8400 (mmtm) REVERT: L 103 LYS cc_start: 0.8710 (tttt) cc_final: 0.8105 (tptp) REVERT: H 17 SER cc_start: 0.8870 (p) cc_final: 0.8661 (m) REVERT: H 89 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: A 129 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8438 (mtmt) REVERT: A 287 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8653 (t0) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 1.2001 time to fit residues: 80.4796 Evaluate side-chains 63 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.083818 restraints weight = 4356.416| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.59 r_work: 0.2688 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3691 Z= 0.360 Angle : 0.599 8.795 5011 Z= 0.303 Chirality : 0.048 0.176 561 Planarity : 0.004 0.036 631 Dihedral : 6.026 51.817 588 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.32 % Allowed : 11.08 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.14 (0.41), residues: 431 helix: 3.64 (1.80), residues: 11 sheet: 1.45 (0.38), residues: 189 loop : 0.06 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.012 0.002 TYR A 279 ARG 0.003 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.367 Fit side-chains REVERT: L 30 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.7910 (mtm180) REVERT: H 17 SER cc_start: 0.8905 (p) cc_final: 0.8675 (m) REVERT: H 89 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: H 114 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: A 102 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7866 (mtp85) REVERT: A 129 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8471 (mtmt) REVERT: A 287 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8362 (t0) outliers start: 9 outliers final: 3 residues processed: 58 average time/residue: 1.3165 time to fit residues: 78.6960 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 39 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 8 optimal weight: 0.0970 overall best weight: 0.1694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.108272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.091660 restraints weight = 4228.017| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.46 r_work: 0.2802 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3691 Z= 0.163 Angle : 0.495 6.720 5011 Z= 0.254 Chirality : 0.044 0.141 561 Planarity : 0.004 0.035 631 Dihedral : 5.005 43.191 588 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 11.86 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.42), residues: 431 helix: 3.38 (1.75), residues: 11 sheet: 1.42 (0.37), residues: 195 loop : 0.13 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.010 0.001 TYR H 95 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.431 Fit side-chains REVERT: L 30 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.7820 (mtm180) REVERT: L 42 LYS cc_start: 0.8843 (mptt) cc_final: 0.8391 (mmtm) REVERT: H 89 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 129 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8438 (mtmt) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 1.2733 time to fit residues: 86.6943 Evaluate side-chains 60 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.101361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.082860 restraints weight = 4329.541| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.62 r_work: 0.2650 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 3691 Z= 0.469 Angle : 0.649 8.517 5011 Z= 0.327 Chirality : 0.049 0.143 561 Planarity : 0.004 0.036 631 Dihedral : 5.338 34.656 588 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.55 % Allowed : 12.89 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.99 (0.41), residues: 431 helix: 3.47 (1.79), residues: 11 sheet: 1.32 (0.38), residues: 189 loop : -0.01 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.014 0.002 TYR A 279 ARG 0.003 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.416 Fit side-chains REVERT: L 30 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.7838 (mtm180) REVERT: L 93 ASN cc_start: 0.8749 (p0) cc_final: 0.8534 (p0) REVERT: H 89 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: H 103 ARG cc_start: 0.9179 (mmm160) cc_final: 0.8834 (mmm160) REVERT: H 114 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: A 129 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8483 (mtmt) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 1.2989 time to fit residues: 75.0184 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 6 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.084014 restraints weight = 4328.976| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.63 r_work: 0.2684 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3691 Z= 0.319 Angle : 0.580 7.716 5011 Z= 0.295 Chirality : 0.047 0.139 561 Planarity : 0.004 0.036 631 Dihedral : 4.903 28.495 588 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.80 % Allowed : 13.92 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.97 (0.41), residues: 431 helix: 3.45 (1.80), residues: 11 sheet: 1.28 (0.38), residues: 189 loop : -0.00 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.014 0.002 PHE A 133 TYR 0.012 0.002 TYR H 95 ARG 0.003 0.000 ARG H 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.415 Fit side-chains REVERT: L 30 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.7865 (mtm180) REVERT: L 42 LYS cc_start: 0.8890 (mptt) cc_final: 0.8399 (mmtm) REVERT: L 93 ASN cc_start: 0.8695 (p0) cc_final: 0.8488 (p0) REVERT: H 89 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: H 114 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: A 129 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8484 (mtmt) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 1.2405 time to fit residues: 70.4648 Evaluate side-chains 57 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 7 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.084442 restraints weight = 4346.747| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.58 r_work: 0.2693 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3691 Z= 0.318 Angle : 0.587 7.816 5011 Z= 0.297 Chirality : 0.046 0.140 561 Planarity : 0.004 0.036 631 Dihedral : 4.719 20.934 588 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.32 % Allowed : 13.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.99 (0.41), residues: 431 helix: 3.50 (1.81), residues: 11 sheet: 1.32 (0.38), residues: 189 loop : -0.02 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.002 PHE A 133 TYR 0.012 0.002 TYR H 95 ARG 0.002 0.000 ARG H 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.69 seconds wall clock time: 57 minutes 46.90 seconds (3466.90 seconds total)