Starting phenix.real_space_refine on Tue Feb 11 01:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt6_18644/02_2025/8qt6_18644.cif" } resolution = 2.29 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= 0.101 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 11 5.16 5 C 2261 2.51 5 N 548 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3466 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3264 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 202 Unusual residues: {'FAD': 1, 'HEM': 2} Classifications: {'undetermined': 3, 'water': 63} Link IDs: {None: 65} Time building chain proxies: 3.08, per 1000 atoms: 0.89 Number of scatterers: 3466 At special positions: 0 Unit cell: (62.1736, 67.1876, 92.2576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 11 16.00 P 2 15.00 O 642 8.00 N 548 7.00 C 2261 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 364.7 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 56.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 115 removed outlier: 3.570A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.642A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 removed outlier: 3.921A pdb=" N ALA A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.708A pdb=" N LYS A 268 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.865A pdb=" N GLN A 287 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR A 316 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP A 289 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER A 318 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 291 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 365 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE A 393 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 367 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU A 395 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET A 369 " --> pdb=" O GLU A 395 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 540 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: 0.87 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 1504 1.39 - 1.56: 1981 1.56 - 1.73: 4 1.73 - 1.89: 21 1.89 - 2.06: 8 Bond restraints: 3518 Sorted by residual: bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.588 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.563 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O5' FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.637 1.572 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3P FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.633 1.586 0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.492 1.531 -0.039 2.00e-02 2.50e+03 3.75e+00 ... (remaining 3513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 4683 1.44 - 2.89: 75 2.89 - 4.33: 27 4.33 - 5.78: 13 5.78 - 7.22: 3 Bond angle restraints: 4801 Sorted by residual: angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 115.28 7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" O1A FAD A 501 " pdb=" PA FAD A 501 " pdb=" O5B FAD A 501 " ideal model delta sigma weight residual 104.10 110.80 -6.70 3.00e+00 1.11e-01 4.98e+00 angle pdb=" CA LEU A 187 " pdb=" CB LEU A 187 " pdb=" CG LEU A 187 " ideal model delta sigma weight residual 116.30 123.09 -6.79 3.50e+00 8.16e-02 3.76e+00 angle pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " pdb=" CBB HEM A 503 " ideal model delta sigma weight residual 120.00 125.65 -5.65 3.00e+00 1.11e-01 3.55e+00 angle pdb=" CA TYR A 275 " pdb=" CB TYR A 275 " pdb=" CG TYR A 275 " ideal model delta sigma weight residual 113.90 117.28 -3.38 1.80e+00 3.09e-01 3.54e+00 ... (remaining 4796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 1709 17.72 - 35.45: 201 35.45 - 53.17: 65 53.17 - 70.89: 16 70.89 - 88.62: 11 Dihedral angle restraints: 2002 sinusoidal: 840 harmonic: 1162 Sorted by residual: dihedral pdb=" C2D HEM A 503 " pdb=" C3D HEM A 503 " pdb=" CAD HEM A 503 " pdb=" CBD HEM A 503 " ideal model delta sinusoidal sigma weight residual 0.00 75.35 -75.35 2 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" C1A HEM A 503 " pdb=" C2A HEM A 503 " pdb=" CAA HEM A 503 " pdb=" CBA HEM A 503 " ideal model delta sinusoidal sigma weight residual 0.00 71.87 -71.87 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" C1A HEM A 502 " pdb=" C2A HEM A 502 " pdb=" CAA HEM A 502 " pdb=" CBA HEM A 502 " ideal model delta sinusoidal sigma weight residual -0.00 -71.84 71.84 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 299 0.028 - 0.056: 124 0.056 - 0.085: 47 0.085 - 0.113: 24 0.113 - 0.141: 7 Chirality restraints: 501 Sorted by residual: chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 203 " pdb=" N ILE A 203 " pdb=" C ILE A 203 " pdb=" CB ILE A 203 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA THR A 297 " pdb=" N THR A 297 " pdb=" C THR A 297 " pdb=" CB THR A 297 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 498 not shown) Planarity restraints: 576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 362 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 43 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C SER A 43 " -0.023 2.00e-02 2.50e+03 pdb=" O SER A 43 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 44 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 41 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C SER A 41 " 0.022 2.00e-02 2.50e+03 pdb=" O SER A 41 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 42 " -0.007 2.00e-02 2.50e+03 ... (remaining 573 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 137 2.72 - 3.26: 3332 3.26 - 3.81: 6257 3.81 - 4.35: 8020 4.35 - 4.90: 12844 Nonbonded interactions: 30590 Sorted by model distance: nonbonded pdb=" NE2 HIS A 129 " pdb="FE HEM A 503 " model vdw 2.174 3.080 nonbonded pdb=" O1P FAD A 501 " pdb=" O HOH A 601 " model vdw 2.225 3.040 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 633 " model vdw 2.241 3.040 nonbonded pdb=" O HOH A 606 " pdb=" O HOH A 661 " model vdw 2.250 3.040 nonbonded pdb=" O HOH A 612 " pdb=" O HOH A 620 " model vdw 2.257 3.040 ... (remaining 30585 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: 0.680 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.150 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3518 Z= 0.261 Angle : 0.596 7.222 4801 Z= 0.275 Chirality : 0.040 0.141 501 Planarity : 0.004 0.043 576 Dihedral : 18.307 88.618 1262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.86 % Allowed : 19.02 % Favored : 80.12 % 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: 0.77 (0.44), residues: 397 helix: 0.95 (0.37), residues: 198 sheet: 0.34 (0.54), residues: 89 loop : 0.13 (0.68), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.009 0.001 PHE A 82 TYR 0.014 0.001 TYR A 275 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.392 Fit side-chains REVERT: A 186 TYR cc_start: 0.8912 (m-80) cc_final: 0.8572 (m-80) REVERT: A 385 LYS cc_start: 0.6845 (tttt) cc_final: 0.6543 (ttmp) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.9170 time to fit residues: 45.0038 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 328 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101539 restraints weight = 3347.865| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.23 r_work: 0.3045 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.004 0.054 3518 Z= 0.262 Angle : 0.682 14.892 4801 Z= 0.296 Chirality : 0.042 0.147 501 Planarity : 0.004 0.043 576 Dihedral : 11.219 88.185 504 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.02 % Allowed : 17.00 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.43), residues: 397 helix: 1.87 (0.36), residues: 201 sheet: 0.24 (0.54), residues: 88 loop : 0.13 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 25 HIS 0.008 0.001 HIS A 69 PHE 0.011 0.001 PHE A 82 TYR 0.015 0.002 TYR A 144 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.374 Fit side-chains REVERT: A 285 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: A 320 ARG cc_start: 0.7415 (mtp85) cc_final: 0.7062 (mtp85) REVERT: A 385 LYS cc_start: 0.6939 (tttt) cc_final: 0.6550 (ttmp) outliers start: 7 outliers final: 2 residues processed: 51 average time/residue: 1.0446 time to fit residues: 55.5141 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101279 restraints weight = 3329.832| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.25 r_work: 0.3041 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3518 Z= 0.265 Angle : 0.665 14.533 4801 Z= 0.292 Chirality : 0.042 0.145 501 Planarity : 0.003 0.041 576 Dihedral : 11.107 83.464 499 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 15.85 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.42), residues: 397 helix: 1.76 (0.36), residues: 202 sheet: 0.20 (0.53), residues: 88 loop : -0.01 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.011 0.001 PHE A 211 TYR 0.015 0.002 TYR A 275 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.416 Fit side-chains REVERT: A 110 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 285 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: A 320 ARG cc_start: 0.7317 (mtp85) cc_final: 0.6941 (mtp85) outliers start: 8 outliers final: 2 residues processed: 52 average time/residue: 1.0694 time to fit residues: 57.8635 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101257 restraints weight = 3352.019| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.30 r_work: 0.3040 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3518 Z= 0.214 Angle : 0.619 14.110 4801 Z= 0.271 Chirality : 0.041 0.144 501 Planarity : 0.003 0.040 576 Dihedral : 10.511 79.894 499 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.02 % Allowed : 17.58 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.42), residues: 397 helix: 1.88 (0.36), residues: 202 sheet: 0.16 (0.54), residues: 88 loop : 0.03 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.009 0.001 PHE A 218 TYR 0.014 0.002 TYR A 275 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.367 Fit side-chains REVERT: A 110 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (mp) REVERT: A 272 ASP cc_start: 0.8772 (p0) cc_final: 0.8517 (p0) outliers start: 7 outliers final: 1 residues processed: 49 average time/residue: 0.8284 time to fit residues: 42.6742 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.124108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102643 restraints weight = 3415.959| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.30 r_work: 0.3060 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3518 Z= 0.181 Angle : 0.589 13.423 4801 Z= 0.258 Chirality : 0.040 0.141 501 Planarity : 0.003 0.040 576 Dihedral : 9.845 80.308 499 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 17.87 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.42), residues: 397 helix: 1.98 (0.36), residues: 202 sheet: 0.15 (0.54), residues: 88 loop : 0.08 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.009 0.001 PHE A 82 TYR 0.014 0.001 TYR A 275 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.417 Fit side-chains REVERT: A 110 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 272 ASP cc_start: 0.8761 (p0) cc_final: 0.8520 (p0) REVERT: A 285 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7711 (tp30) outliers start: 6 outliers final: 0 residues processed: 50 average time/residue: 1.0637 time to fit residues: 55.3755 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.122965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101670 restraints weight = 3414.860| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.28 r_work: 0.3049 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3518 Z= 0.214 Angle : 0.620 14.036 4801 Z= 0.271 Chirality : 0.041 0.142 501 Planarity : 0.003 0.040 576 Dihedral : 10.226 78.394 499 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 18.73 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.42), residues: 397 helix: 1.88 (0.36), residues: 202 sheet: 0.13 (0.54), residues: 88 loop : 0.05 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.012 0.001 PHE A 82 TYR 0.015 0.002 TYR A 275 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.386 Fit side-chains REVERT: A 110 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 149 ASN cc_start: 0.7943 (m-40) cc_final: 0.7564 (t0) REVERT: A 272 ASP cc_start: 0.8772 (p0) cc_final: 0.8516 (p0) REVERT: A 285 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7681 (tp30) outliers start: 6 outliers final: 1 residues processed: 49 average time/residue: 0.9077 time to fit residues: 46.4910 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.122440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100813 restraints weight = 3363.240| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.30 r_work: 0.3035 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3518 Z= 0.247 Angle : 0.647 14.128 4801 Z= 0.286 Chirality : 0.042 0.143 501 Planarity : 0.003 0.040 576 Dihedral : 10.568 78.176 499 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 18.73 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.42), residues: 397 helix: 1.78 (0.35), residues: 202 sheet: 0.13 (0.53), residues: 88 loop : -0.01 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.012 0.001 PHE A 82 TYR 0.015 0.002 TYR A 275 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.418 Fit side-chains REVERT: A 110 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 272 ASP cc_start: 0.8778 (p0) cc_final: 0.8557 (p0) REVERT: A 285 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7708 (tp30) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.9464 time to fit residues: 48.4266 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103265 restraints weight = 3390.945| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.28 r_work: 0.3074 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3518 Z= 0.181 Angle : 0.592 13.179 4801 Z= 0.260 Chirality : 0.040 0.139 501 Planarity : 0.003 0.039 576 Dihedral : 9.710 80.460 499 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.44 % Allowed : 19.31 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.42), residues: 397 helix: 1.96 (0.36), residues: 202 sheet: 0.13 (0.54), residues: 88 loop : 0.09 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.009 0.001 PHE A 85 TYR 0.014 0.001 TYR A 275 ARG 0.000 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.405 Fit side-chains REVERT: A 110 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 272 ASP cc_start: 0.8753 (p0) cc_final: 0.8513 (p0) REVERT: A 285 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7705 (tp30) outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.9819 time to fit residues: 50.0799 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102380 restraints weight = 3302.571| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.29 r_work: 0.3058 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3518 Z= 0.198 Angle : 0.612 13.690 4801 Z= 0.268 Chirality : 0.040 0.141 501 Planarity : 0.003 0.040 576 Dihedral : 9.952 78.921 499 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.15 % Allowed : 20.46 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.42), residues: 397 helix: 1.91 (0.36), residues: 202 sheet: 0.12 (0.54), residues: 88 loop : 0.07 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 85 TYR 0.014 0.002 TYR A 275 ARG 0.001 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.324 Fit side-chains REVERT: A 110 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7509 (mp) REVERT: A 272 ASP cc_start: 0.8762 (p0) cc_final: 0.8518 (p0) REVERT: A 285 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7717 (tp30) outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 0.9756 time to fit residues: 49.8324 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102155 restraints weight = 3347.282| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.30 r_work: 0.3054 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3518 Z= 0.205 Angle : 0.614 13.610 4801 Z= 0.270 Chirality : 0.041 0.140 501 Planarity : 0.003 0.040 576 Dihedral : 9.994 78.713 499 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.15 % Allowed : 19.88 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.42), residues: 397 helix: 1.89 (0.36), residues: 202 sheet: 0.12 (0.54), residues: 88 loop : 0.07 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.011 0.001 PHE A 85 TYR 0.014 0.002 TYR A 275 ARG 0.000 0.000 ARG A 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.389 Fit side-chains REVERT: A 110 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 272 ASP cc_start: 0.8768 (p0) cc_final: 0.8519 (p0) REVERT: A 285 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7715 (tp30) outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 0.9988 time to fit residues: 50.9804 Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101855 restraints weight = 3347.948| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.31 r_work: 0.3051 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3518 Z= 0.212 Angle : 0.623 13.763 4801 Z= 0.274 Chirality : 0.041 0.141 501 Planarity : 0.003 0.040 576 Dihedral : 10.073 78.475 499 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.86 % Allowed : 20.46 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.42), residues: 397 helix: 1.87 (0.36), residues: 202 sheet: 0.12 (0.54), residues: 88 loop : 0.06 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 69 PHE 0.012 0.001 PHE A 85 TYR 0.014 0.002 TYR A 275 ARG 0.000 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.24 seconds wall clock time: 53 minutes 52.34 seconds (3232.34 seconds total)