Starting phenix.real_space_refine on Mon Jan 13 14:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3l_44144/01_2025/9b3l_44144_neut.cif" } resolution = 3.25 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= 0.037 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 15 5.16 5 C 1768 2.51 5 N 407 2.21 5 O 433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2623 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2623 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 2.75, per 1000 atoms: 1.05 Number of scatterers: 2623 At special positions: 0 Unit cell: (59.4, 70.95, 80.025, 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 15 16.00 O 433 8.00 N 407 7.00 C 1768 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: 0.68 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 644 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.871A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 4.047A pdb=" N LYS A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.887A pdb=" N LEU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.638A pdb=" N LYS A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 88 Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix removed outlier: 3.588A pdb=" N ALA A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 151 removed outlier: 3.630A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.842A pdb=" N TYR A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.630A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 261 Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 326 through 354 Proline residue: A 344 - end of helix removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 233 hydrogen bonds defined for protein. 699 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: 0.74 Time building geometry restraints manager: 0.78 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: 776 1.34 - 1.46: 581 1.46 - 1.58: 1301 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2687 Sorted by residual: bond pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.94e-01 bond pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.77e-01 bond pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.66e-02 3.63e+03 4.30e-01 bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.28e-01 bond pdb=" C MET A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.06e-01 ... (remaining 2682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 3491 1.12 - 2.23: 127 2.23 - 3.35: 16 3.35 - 4.47: 6 4.47 - 5.58: 8 Bond angle restraints: 3648 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 112.90 109.93 2.97 1.31e+00 5.83e-01 5.13e+00 angle pdb=" C TYR A 257 " pdb=" N PHE A 258 " pdb=" CA PHE A 258 " ideal model delta sigma weight residual 122.31 118.74 3.57 2.00e+00 2.50e-01 3.19e+00 angle pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 112.60 114.33 -1.73 1.00e+00 1.00e+00 2.98e+00 angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.16 110.61 2.55 1.49e+00 4.50e-01 2.92e+00 angle pdb=" CA ASP A 385 " pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 112.60 114.30 -1.70 1.00e+00 1.00e+00 2.90e+00 ... (remaining 3643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 1219 11.94 - 23.89: 182 23.89 - 35.83: 79 35.83 - 47.77: 35 47.77 - 59.71: 9 Dihedral angle restraints: 1524 sinusoidal: 514 harmonic: 1010 Sorted by residual: dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " 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=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " pdb=" CG ASN A 137 " ideal model delta sinusoidal sigma weight residual -60.00 -119.71 59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 346 " pdb=" CB ILE A 346 " pdb=" CG1 ILE A 346 " pdb=" CD1 ILE A 346 " ideal model delta sinusoidal sigma weight residual 60.00 115.94 -55.94 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 253 0.027 - 0.054: 95 0.054 - 0.081: 57 0.081 - 0.108: 25 0.108 - 0.134: 4 Chirality restraints: 434 Sorted by residual: chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU A 165 " pdb=" CB LEU A 165 " pdb=" CD1 LEU A 165 " pdb=" CD2 LEU A 165 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 431 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 27 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 344 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 256 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A 257 " 0.008 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 734 2.80 - 3.32: 2727 3.32 - 3.85: 4553 3.85 - 4.37: 4861 4.37 - 4.90: 8619 Nonbonded interactions: 21494 Sorted by model distance: nonbonded pdb=" NZ LYS A 232 " pdb=" O ALA A 289 " model vdw 2.274 3.120 nonbonded pdb=" O SER A 241 " pdb=" OG1 THR A 245 " model vdw 2.304 3.040 nonbonded pdb=" O SER A 122 " pdb=" NZ LYS A 125 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASP A 385 " pdb=" N LEU A 386 " model vdw 2.442 3.120 nonbonded pdb=" OG SER A 133 " pdb=" OG1 THR A 314 " model vdw 2.463 3.040 ... (remaining 21489 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: 1.340 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.120 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 0.022 2687 Z= 0.202 Angle : 0.537 5.582 3648 Z= 0.286 Chirality : 0.040 0.134 434 Planarity : 0.005 0.053 445 Dihedral : 15.962 59.714 880 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.40 % Allowed : 32.41 % Favored : 67.19 % 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: 2.14 (0.46), residues: 350 helix: 2.04 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -2.80 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.012 0.001 PHE A 216 TYR 0.011 0.001 TYR A 228 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.287 Fit side-chains REVERT: A 156 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6315 (ttm-80) REVERT: A 338 MET cc_start: 0.8799 (ttm) cc_final: 0.8526 (ttp) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1187 time to fit residues: 10.4520 Evaluate side-chains 69 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133604 restraints weight = 3592.107| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.94 r_work: 0.3428 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2687 Z= 0.225 Angle : 0.510 5.751 3648 Z= 0.272 Chirality : 0.041 0.125 434 Planarity : 0.005 0.051 445 Dihedral : 4.134 18.130 372 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.14 % Allowed : 29.25 % Favored : 65.61 % 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 (0.45), residues: 350 helix: 2.18 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.66 (0.91), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.013 0.001 PHE A 216 TYR 0.010 0.001 TYR A 360 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.274 Fit side-chains REVERT: A 64 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4712 (tptm) REVERT: A 288 PHE cc_start: 0.7451 (m-80) cc_final: 0.7234 (m-80) REVERT: A 338 MET cc_start: 0.8787 (ttm) cc_final: 0.8544 (ttp) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.1215 time to fit residues: 11.3606 Evaluate side-chains 73 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133300 restraints weight = 3633.276| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.94 r_work: 0.3415 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2687 Z= 0.236 Angle : 0.504 5.482 3648 Z= 0.267 Chirality : 0.041 0.121 434 Planarity : 0.004 0.049 445 Dihedral : 4.127 19.199 370 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.32 % Allowed : 26.09 % Favored : 67.59 % 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: 2.56 (0.45), residues: 350 helix: 2.23 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.64 (0.90), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.013 0.001 PHE A 159 TYR 0.011 0.001 TYR A 360 ARG 0.003 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.270 Fit side-chains REVERT: A 64 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4683 (tptm) REVERT: A 288 PHE cc_start: 0.7401 (m-80) cc_final: 0.7045 (m-80) REVERT: A 338 MET cc_start: 0.8805 (ttm) cc_final: 0.8596 (ttp) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.1177 time to fit residues: 11.1753 Evaluate side-chains 75 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134089 restraints weight = 3622.573| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.98 r_work: 0.3425 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2687 Z= 0.194 Angle : 0.508 7.477 3648 Z= 0.262 Chirality : 0.040 0.125 434 Planarity : 0.004 0.046 445 Dihedral : 4.090 19.858 370 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.93 % Allowed : 27.27 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.46), residues: 350 helix: 2.32 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.48 (0.93), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.012 0.001 PHE A 335 TYR 0.012 0.001 TYR A 360 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.294 Fit side-chains REVERT: A 64 LYS cc_start: 0.4849 (OUTLIER) cc_final: 0.4562 (tptm) REVERT: A 160 TYR cc_start: 0.7790 (m-80) cc_final: 0.7510 (m-80) REVERT: A 288 PHE cc_start: 0.7304 (m-80) cc_final: 0.6881 (m-80) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1216 time to fit residues: 12.5470 Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.168158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135821 restraints weight = 3615.626| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.97 r_work: 0.3449 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2687 Z= 0.168 Angle : 0.518 6.517 3648 Z= 0.263 Chirality : 0.040 0.134 434 Planarity : 0.004 0.045 445 Dihedral : 4.031 20.087 370 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.53 % Allowed : 28.85 % Favored : 65.61 % 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 (0.46), residues: 350 helix: 2.40 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.40 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.011 0.001 PHE A 335 TYR 0.008 0.001 TYR A 160 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.286 Fit side-chains REVERT: A 64 LYS cc_start: 0.4807 (OUTLIER) cc_final: 0.4512 (tptm) REVERT: A 156 ARG cc_start: 0.6601 (ttm-80) cc_final: 0.6202 (ttm-80) REVERT: A 160 TYR cc_start: 0.7695 (m-80) cc_final: 0.7176 (m-80) REVERT: A 288 PHE cc_start: 0.7173 (m-80) cc_final: 0.6708 (m-80) REVERT: A 341 PHE cc_start: 0.7620 (t80) cc_final: 0.7408 (t80) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.1121 time to fit residues: 11.8486 Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133042 restraints weight = 3662.772| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.95 r_work: 0.3411 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2687 Z= 0.243 Angle : 0.553 5.454 3648 Z= 0.283 Chirality : 0.043 0.274 434 Planarity : 0.004 0.044 445 Dihedral : 4.064 20.021 370 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.32 % Allowed : 28.85 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.62 (0.45), residues: 350 helix: 2.27 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.45 (0.89), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 293 HIS 0.002 0.001 HIS A 155 PHE 0.015 0.002 PHE A 335 TYR 0.009 0.001 TYR A 160 ARG 0.002 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.275 Fit side-chains REVERT: A 64 LYS cc_start: 0.4843 (OUTLIER) cc_final: 0.4539 (tptm) REVERT: A 288 PHE cc_start: 0.7221 (m-80) cc_final: 0.6748 (m-80) REVERT: A 346 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7485 (mt) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.1160 time to fit residues: 10.4577 Evaluate side-chains 74 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134321 restraints weight = 3723.771| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.04 r_work: 0.3416 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2687 Z= 0.207 Angle : 0.552 5.951 3648 Z= 0.281 Chirality : 0.042 0.227 434 Planarity : 0.004 0.043 445 Dihedral : 4.087 20.202 370 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.32 % Allowed : 29.25 % Favored : 64.43 % 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: 2.65 (0.46), residues: 350 helix: 2.29 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.40 (0.89), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.014 0.001 PHE A 335 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.308 Fit side-chains REVERT: A 64 LYS cc_start: 0.4847 (OUTLIER) cc_final: 0.4508 (tptm) REVERT: A 288 PHE cc_start: 0.7279 (m-80) cc_final: 0.6775 (m-80) REVERT: A 341 PHE cc_start: 0.7586 (t80) cc_final: 0.7224 (t80) REVERT: A 346 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7395 (mt) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.1218 time to fit residues: 11.5494 Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132901 restraints weight = 3611.779| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2687 Z= 0.256 Angle : 0.568 6.151 3648 Z= 0.290 Chirality : 0.043 0.222 434 Planarity : 0.004 0.042 445 Dihedral : 4.140 20.279 370 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 6.32 % Allowed : 30.04 % Favored : 63.64 % 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: 2.50 (0.45), residues: 350 helix: 2.19 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.42 (0.86), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.017 0.001 PHE A 159 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.299 Fit side-chains REVERT: A 64 LYS cc_start: 0.4807 (OUTLIER) cc_final: 0.4491 (tptm) REVERT: A 288 PHE cc_start: 0.7213 (m-80) cc_final: 0.6664 (m-80) outliers start: 16 outliers final: 13 residues processed: 75 average time/residue: 0.1211 time to fit residues: 11.2044 Evaluate side-chains 76 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132489 restraints weight = 3638.681| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.00 r_work: 0.3395 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2687 Z= 0.251 Angle : 0.587 6.479 3648 Z= 0.297 Chirality : 0.043 0.208 434 Planarity : 0.004 0.042 445 Dihedral : 4.189 20.243 370 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.93 % Allowed : 30.04 % Favored : 64.03 % 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 (0.45), residues: 350 helix: 2.12 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.38 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.016 0.001 PHE A 159 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.298 Fit side-chains REVERT: A 64 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.4491 (tptm) REVERT: A 71 ILE cc_start: 0.8304 (mp) cc_final: 0.7817 (mt) REVERT: A 288 PHE cc_start: 0.7239 (m-80) cc_final: 0.6669 (m-80) outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1298 time to fit residues: 11.8782 Evaluate side-chains 75 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131781 restraints weight = 3625.464| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.97 r_work: 0.3404 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2687 Z= 0.227 Angle : 0.595 6.576 3648 Z= 0.298 Chirality : 0.043 0.202 434 Planarity : 0.004 0.042 445 Dihedral : 4.215 20.492 370 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.93 % Allowed : 30.04 % Favored : 64.03 % 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 (0.45), residues: 350 helix: 2.13 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.33 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.014 0.001 PHE A 159 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.001 ARG A 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.288 Fit side-chains REVERT: A 64 LYS cc_start: 0.4794 (OUTLIER) cc_final: 0.4455 (tptm) REVERT: A 71 ILE cc_start: 0.8273 (mp) cc_final: 0.7748 (mt) REVERT: A 288 PHE cc_start: 0.7225 (m-80) cc_final: 0.6748 (m-80) REVERT: A 341 PHE cc_start: 0.7269 (t80) cc_final: 0.7010 (t80) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1225 time to fit residues: 11.2734 Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132271 restraints weight = 3642.834| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.99 r_work: 0.3389 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2687 Z= 0.273 Angle : 0.607 6.402 3648 Z= 0.307 Chirality : 0.043 0.204 434 Planarity : 0.004 0.042 445 Dihedral : 4.272 20.175 370 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.93 % Allowed : 30.83 % Favored : 63.24 % 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: 2.24 (0.45), residues: 350 helix: 2.00 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.38 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.017 0.002 PHE A 159 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.001 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.58 seconds wall clock time: 29 minutes 21.69 seconds (1761.69 seconds total)