Starting phenix.real_space_refine on Fri May 9 16:08:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh2_44530/05_2025/9bh2_44530.cif" } resolution = 2.7 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= 0.001 sd= 0.019 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 17 5.16 5 C 2028 2.51 5 N 498 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3078 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3078 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.87, per 1000 atoms: 0.93 Number of scatterers: 3078 At special positions: 0 Unit cell: (67.68, 70.218, 80.37, 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 17 16.00 O 535 8.00 N 498 7.00 C 2028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 388.8 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 89.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 11 through 34 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 43 through 73 removed outlier: 3.776A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 74 through 108 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.563A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.506A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.591A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.363A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.748A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.058A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.637A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 958 1.34 - 1.46: 640 1.46 - 1.58: 1508 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 3139 Sorted by residual: bond pdb=" N LEU A 3 " pdb=" CA LEU A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.461 1.452 0.009 1.07e-02 8.73e+03 6.86e-01 bond pdb=" CB GLU A 172 " pdb=" CG GLU A 172 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.18e-01 bond pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.31e-02 5.83e+03 4.62e-01 bond pdb=" C PRO A 128 " pdb=" O PRO A 128 " ideal model delta sigma weight residual 1.246 1.240 0.005 8.50e-03 1.38e+04 4.11e-01 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4048 0.92 - 1.84: 173 1.84 - 2.75: 33 2.75 - 3.67: 12 3.67 - 4.59: 15 Bond angle restraints: 4281 Sorted by residual: angle pdb=" C VAL A 370 " pdb=" CA VAL A 370 " pdb=" CB VAL A 370 " ideal model delta sigma weight residual 112.14 109.38 2.76 1.35e+00 5.49e-01 4.18e+00 angle pdb=" N GLN A 220 " pdb=" CA GLN A 220 " pdb=" C GLN A 220 " ideal model delta sigma weight residual 110.80 115.14 -4.34 2.13e+00 2.20e-01 4.15e+00 angle pdb=" CA GLN A 123 " pdb=" CB GLN A 123 " pdb=" CG GLN A 123 " ideal model delta sigma weight residual 114.10 118.00 -3.90 2.00e+00 2.50e-01 3.81e+00 angle pdb=" CA GLU A 172 " pdb=" CB GLU A 172 " pdb=" CG GLU A 172 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.74e+00 angle pdb=" N SER A 72 " pdb=" CA SER A 72 " pdb=" C SER A 72 " ideal model delta sigma weight residual 111.36 113.36 -2.00 1.09e+00 8.42e-01 3.38e+00 ... (remaining 4276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1638 17.76 - 35.52: 156 35.52 - 53.29: 36 53.29 - 71.05: 10 71.05 - 88.81: 5 Dihedral angle restraints: 1845 sinusoidal: 668 harmonic: 1177 Sorted by residual: dihedral pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" N VAL A 335 " pdb=" CA VAL A 335 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU A 219 " pdb=" C GLU A 219 " pdb=" N GLN A 220 " pdb=" CA GLN A 220 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " pdb=" CD GLU A 227 " pdb=" OE1 GLU A 227 " ideal model delta sinusoidal sigma weight residual 0.00 -84.35 84.35 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 315 0.026 - 0.052: 119 0.052 - 0.078: 78 0.078 - 0.105: 18 0.105 - 0.131: 7 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA VAL A 138 " pdb=" N VAL A 138 " pdb=" C VAL A 138 " pdb=" CB VAL A 138 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 534 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 242 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" C GLN A 242 " -0.020 2.00e-02 2.50e+03 pdb=" O GLN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 243 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 217 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C MET A 217 " 0.020 2.00e-02 2.50e+03 pdb=" O MET A 217 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 218 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C VAL A 39 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL A 39 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS A 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 48 2.66 - 3.22: 3291 3.22 - 3.78: 5230 3.78 - 4.34: 6712 4.34 - 4.90: 11144 Nonbonded interactions: 26425 Sorted by model distance: nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.104 3.040 nonbonded pdb=" N GLU A 172 " pdb=" OE1 GLU A 172 " model vdw 2.110 3.120 nonbonded pdb=" OD1 ASN A 148 " pdb=" NE2 GLN A 150 " model vdw 2.113 3.120 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.330 3.040 ... (remaining 26420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.040 Find NCS groups from input model: 0.030 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.003 0.033 3139 Z= 0.138 Angle : 0.523 4.588 4281 Z= 0.279 Chirality : 0.038 0.131 537 Planarity : 0.002 0.020 526 Dihedral : 15.814 88.811 1099 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.62 % Allowed : 19.50 % Favored : 79.88 % 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: 2.82 (0.41), residues: 412 helix: 2.18 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.07 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 332 PHE 0.006 0.001 PHE A 157 TYR 0.010 0.001 TYR A 299 ARG 0.001 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.11483 ( 266) hydrogen bonds : angle 5.14965 ( 792) covalent geometry : bond 0.00283 ( 3139) covalent geometry : angle 0.52343 ( 4281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.323 Fit side-chains REVERT: A 33 TYR cc_start: 0.8424 (m-80) cc_final: 0.8162 (m-80) REVERT: A 61 ILE cc_start: 0.8054 (tt) cc_final: 0.7778 (tt) REVERT: A 91 LEU cc_start: 0.8373 (tt) cc_final: 0.8157 (tp) REVERT: A 179 SER cc_start: 0.7689 (t) cc_final: 0.7258 (p) REVERT: A 311 MET cc_start: 0.7570 (mmp) cc_final: 0.7303 (mmt) REVERT: A 369 SER cc_start: 0.8718 (t) cc_final: 0.8414 (p) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.7303 time to fit residues: 68.4938 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 123 GLN A 203 GLN A 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101640 restraints weight = 5374.106| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.50 r_work: 0.3451 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3139 Z= 0.157 Angle : 0.614 6.077 4281 Z= 0.310 Chirality : 0.045 0.332 537 Planarity : 0.004 0.034 526 Dihedral : 3.864 21.626 440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.57 % Allowed : 18.58 % Favored : 75.85 % 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: 2.63 (0.39), residues: 412 helix: 2.03 (0.26), residues: 353 sheet: None (None), residues: 0 loop : 0.14 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 368 PHE 0.013 0.001 PHE A 323 TYR 0.026 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 266) hydrogen bonds : angle 4.55162 ( 792) covalent geometry : bond 0.00366 ( 3139) covalent geometry : angle 0.61405 ( 4281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.323 Fit side-chains REVERT: A 10 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 59 MET cc_start: 0.8268 (mmm) cc_final: 0.8017 (tpt) REVERT: A 61 ILE cc_start: 0.8458 (tt) cc_final: 0.8165 (tt) REVERT: A 102 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7927 (mt) REVERT: A 179 SER cc_start: 0.8201 (t) cc_final: 0.7979 (p) REVERT: A 245 LEU cc_start: 0.7943 (mt) cc_final: 0.7695 (mt) REVERT: A 311 MET cc_start: 0.7706 (mmp) cc_final: 0.7505 (mmt) outliers start: 18 outliers final: 3 residues processed: 95 average time/residue: 0.7026 time to fit residues: 69.6296 Evaluate side-chains 82 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101784 restraints weight = 5439.820| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.52 r_work: 0.3451 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3139 Z= 0.149 Angle : 0.612 7.868 4281 Z= 0.303 Chirality : 0.043 0.240 537 Planarity : 0.004 0.043 526 Dihedral : 3.905 21.642 440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.95 % Allowed : 18.58 % Favored : 76.47 % 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: 2.42 (0.39), residues: 412 helix: 1.85 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.33 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 332 PHE 0.012 0.001 PHE A 323 TYR 0.023 0.002 TYR A 299 ARG 0.004 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 266) hydrogen bonds : angle 4.51011 ( 792) covalent geometry : bond 0.00349 ( 3139) covalent geometry : angle 0.61202 ( 4281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.352 Fit side-chains REVERT: A 10 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 33 TYR cc_start: 0.8418 (m-80) cc_final: 0.8208 (m-80) REVERT: A 196 LYS cc_start: 0.8140 (mmtt) cc_final: 0.6915 (pttt) REVERT: A 207 ILE cc_start: 0.8990 (mt) cc_final: 0.8784 (mm) REVERT: A 245 LEU cc_start: 0.7993 (mt) cc_final: 0.7775 (mp) outliers start: 16 outliers final: 7 residues processed: 93 average time/residue: 0.8304 time to fit residues: 80.2980 Evaluate side-chains 87 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 chunk 23 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101567 restraints weight = 5402.698| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.52 r_work: 0.3452 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3139 Z= 0.143 Angle : 0.605 7.912 4281 Z= 0.298 Chirality : 0.044 0.292 537 Planarity : 0.005 0.047 526 Dihedral : 3.904 21.938 440 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.57 % Allowed : 21.67 % Favored : 72.76 % 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: 2.36 (0.38), residues: 412 helix: 1.80 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.38 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 332 PHE 0.009 0.001 PHE A 210 TYR 0.023 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 266) hydrogen bonds : angle 4.55816 ( 792) covalent geometry : bond 0.00331 ( 3139) covalent geometry : angle 0.60523 ( 4281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.365 Fit side-chains REVERT: A 10 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 55 LYS cc_start: 0.6142 (ttpt) cc_final: 0.5109 (ttpp) REVERT: A 61 ILE cc_start: 0.8365 (tt) cc_final: 0.8148 (tt) REVERT: A 102 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7937 (mt) REVERT: A 207 ILE cc_start: 0.8980 (mt) cc_final: 0.8779 (mm) REVERT: A 390 ASP cc_start: 0.8256 (t0) cc_final: 0.8054 (t0) outliers start: 18 outliers final: 5 residues processed: 80 average time/residue: 0.8017 time to fit residues: 66.7855 Evaluate side-chains 79 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102707 restraints weight = 5358.967| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.50 r_work: 0.3472 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3139 Z= 0.129 Angle : 0.578 6.827 4281 Z= 0.285 Chirality : 0.041 0.142 537 Planarity : 0.004 0.049 526 Dihedral : 3.849 21.126 440 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.57 % Allowed : 21.05 % Favored : 73.37 % 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: 2.43 (0.39), residues: 412 helix: 1.85 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.37 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 332 PHE 0.009 0.001 PHE A 210 TYR 0.023 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 266) hydrogen bonds : angle 4.47606 ( 792) covalent geometry : bond 0.00291 ( 3139) covalent geometry : angle 0.57767 ( 4281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.486 Fit side-chains REVERT: A 10 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 15 LYS cc_start: 0.8370 (mtmp) cc_final: 0.8155 (mtmt) REVERT: A 33 TYR cc_start: 0.8429 (m-80) cc_final: 0.8227 (m-80) REVERT: A 55 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5820 (ttpt) REVERT: A 196 LYS cc_start: 0.8134 (mmtt) cc_final: 0.6849 (pttt) outliers start: 18 outliers final: 4 residues processed: 87 average time/residue: 0.7778 time to fit residues: 70.3972 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102300 restraints weight = 5522.849| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.64 r_work: 0.3455 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3139 Z= 0.159 Angle : 0.650 8.510 4281 Z= 0.315 Chirality : 0.045 0.354 537 Planarity : 0.005 0.047 526 Dihedral : 3.921 21.272 440 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.95 % Allowed : 21.67 % Favored : 73.37 % 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: 2.39 (0.39), residues: 412 helix: 1.79 (0.25), residues: 354 sheet: None (None), residues: 0 loop : 0.56 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 332 PHE 0.015 0.002 PHE A 122 TYR 0.023 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 266) hydrogen bonds : angle 4.55402 ( 792) covalent geometry : bond 0.00376 ( 3139) covalent geometry : angle 0.65027 ( 4281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.331 Fit side-chains REVERT: A 10 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8111 (t80) REVERT: A 55 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.4879 (ttpt) REVERT: A 361 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8112 (pt) outliers start: 16 outliers final: 5 residues processed: 77 average time/residue: 0.6426 time to fit residues: 51.9839 Evaluate side-chains 80 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104489 restraints weight = 5407.386| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.54 r_work: 0.3494 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3139 Z= 0.125 Angle : 0.617 7.861 4281 Z= 0.299 Chirality : 0.042 0.123 537 Planarity : 0.005 0.044 526 Dihedral : 3.912 19.877 440 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.64 % Allowed : 22.60 % Favored : 72.76 % 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: 2.45 (0.38), residues: 412 helix: 1.87 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.31 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.009 0.001 PHE A 210 TYR 0.021 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 266) hydrogen bonds : angle 4.44240 ( 792) covalent geometry : bond 0.00280 ( 3139) covalent geometry : angle 0.61666 ( 4281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.297 Fit side-chains REVERT: A 10 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 33 TYR cc_start: 0.8425 (m-80) cc_final: 0.8199 (m-80) REVERT: A 49 LEU cc_start: 0.8455 (tm) cc_final: 0.8206 (tp) REVERT: A 55 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5743 (ttpt) REVERT: A 115 LEU cc_start: 0.8529 (mm) cc_final: 0.8273 (mm) REVERT: A 196 LYS cc_start: 0.8125 (mmtt) cc_final: 0.6869 (pttt) REVERT: A 244 LEU cc_start: 0.7694 (mm) cc_final: 0.7462 (mp) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.7369 time to fit residues: 66.8109 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 14 optimal weight: 0.0470 chunk 12 optimal weight: 0.0030 chunk 21 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 overall best weight: 0.0766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104934 restraints weight = 5326.941| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.56 r_work: 0.3500 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3139 Z= 0.128 Angle : 0.638 9.510 4281 Z= 0.309 Chirality : 0.045 0.365 537 Planarity : 0.005 0.042 526 Dihedral : 3.874 19.678 440 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.72 % Allowed : 23.84 % Favored : 72.45 % 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: 2.48 (0.39), residues: 412 helix: 1.92 (0.25), residues: 352 sheet: None (None), residues: 0 loop : 0.12 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 332 PHE 0.009 0.001 PHE A 210 TYR 0.021 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 266) hydrogen bonds : angle 4.42504 ( 792) covalent geometry : bond 0.00287 ( 3139) covalent geometry : angle 0.63820 ( 4281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.358 Fit side-chains REVERT: A 10 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 29 ILE cc_start: 0.8020 (mm) cc_final: 0.7739 (mp) REVERT: A 55 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.4457 (ttpp) REVERT: A 99 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 115 LEU cc_start: 0.8555 (mm) cc_final: 0.8290 (mm) REVERT: A 244 LEU cc_start: 0.7695 (mm) cc_final: 0.7472 (mp) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 0.6170 time to fit residues: 52.5590 Evaluate side-chains 85 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.0050 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104670 restraints weight = 5350.984| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.55 r_work: 0.3495 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3139 Z= 0.137 Angle : 0.629 7.223 4281 Z= 0.304 Chirality : 0.043 0.183 537 Planarity : 0.005 0.043 526 Dihedral : 3.882 19.846 440 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.41 % Allowed : 25.08 % Favored : 71.52 % 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: 2.52 (0.39), residues: 412 helix: 1.98 (0.25), residues: 351 sheet: None (None), residues: 0 loop : 0.00 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 332 PHE 0.009 0.001 PHE A 210 TYR 0.022 0.002 TYR A 299 ARG 0.005 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 266) hydrogen bonds : angle 4.45847 ( 792) covalent geometry : bond 0.00322 ( 3139) covalent geometry : angle 0.62937 ( 4281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.327 Fit side-chains REVERT: A 10 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 49 LEU cc_start: 0.8439 (tm) cc_final: 0.8180 (tp) REVERT: A 55 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5750 (ttpt) REVERT: A 99 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7609 (mp) REVERT: A 115 LEU cc_start: 0.8565 (mm) cc_final: 0.8276 (mm) REVERT: A 196 LYS cc_start: 0.8092 (mmtt) cc_final: 0.6827 (pttt) REVERT: A 244 LEU cc_start: 0.7723 (mm) cc_final: 0.7503 (mp) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 0.7133 time to fit residues: 61.7865 Evaluate side-chains 81 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.0570 chunk 13 optimal weight: 0.0770 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.109603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103482 restraints weight = 5304.593| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.52 r_work: 0.3476 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3139 Z= 0.163 Angle : 0.678 10.820 4281 Z= 0.326 Chirality : 0.046 0.356 537 Planarity : 0.005 0.043 526 Dihedral : 3.890 19.693 440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.41 % Allowed : 25.70 % Favored : 70.90 % 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: 2.41 (0.39), residues: 412 helix: 1.90 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -0.03 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 332 PHE 0.009 0.001 PHE A 323 TYR 0.022 0.002 TYR A 299 ARG 0.004 0.000 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 266) hydrogen bonds : angle 4.60115 ( 792) covalent geometry : bond 0.00398 ( 3139) covalent geometry : angle 0.67815 ( 4281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.425 Fit side-chains REVERT: A 10 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7972 (t80) REVERT: A 15 LYS cc_start: 0.8436 (mtmp) cc_final: 0.8207 (mtmp) REVERT: A 33 TYR cc_start: 0.8405 (m-80) cc_final: 0.8160 (m-80) REVERT: A 49 LEU cc_start: 0.8507 (tm) cc_final: 0.8242 (tp) REVERT: A 55 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5850 (ttpt) REVERT: A 115 LEU cc_start: 0.8585 (mm) cc_final: 0.8291 (mm) REVERT: A 196 LYS cc_start: 0.8127 (mmtt) cc_final: 0.6886 (pttt) REVERT: A 244 LEU cc_start: 0.7750 (mm) cc_final: 0.7540 (mp) REVERT: A 263 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7243 (mmmm) outliers start: 11 outliers final: 3 residues processed: 82 average time/residue: 0.7365 time to fit residues: 62.9015 Evaluate side-chains 81 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102612 restraints weight = 5375.247| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.54 r_work: 0.3460 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3139 Z= 0.178 Angle : 0.672 7.974 4281 Z= 0.325 Chirality : 0.044 0.167 537 Planarity : 0.005 0.043 526 Dihedral : 3.925 19.683 440 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.79 % Allowed : 26.32 % Favored : 70.90 % 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: 2.38 (0.39), residues: 412 helix: 1.88 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -0.04 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 332 PHE 0.009 0.002 PHE A 323 TYR 0.029 0.002 TYR A 215 ARG 0.005 0.001 ARG A 397 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 266) hydrogen bonds : angle 4.64701 ( 792) covalent geometry : bond 0.00438 ( 3139) covalent geometry : angle 0.67208 ( 4281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.28 seconds wall clock time: 44 minutes 12.08 seconds (2652.08 seconds total)