Starting phenix.real_space_refine on Fri May 9 19:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt6_18644/05_2025/8qt6_18644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt6_18644/05_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_18644/05_2025/8qt6_18644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt6_18644/05_2025/8qt6_18644.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt6_18644/05_2025/8qt6_18644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt6_18644/05_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-5687/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: 2.86, per 1000 atoms: 0.83 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: 0.99 Conformation dependent library (CDL) restraints added in 390.5 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: 0.34 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: 0.95 Time building geometry restraints manager: 1.12 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: 0.710 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- 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 : 0.005 0.106 3520 Z= 0.189 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 Details of bonding type rmsd hydrogen bonds : bond 0.13302 ( 187) hydrogen bonds : angle 6.85087 ( 540) covalent geometry : bond 0.00411 ( 3518) covalent geometry : angle 0.59637 ( 4801) Misc. bond : bond 0.08250 ( 2) *********************** 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 : 0.352 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: 0.8750 time to fit residues: 42.9493 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 : 0.342 ------------------------------------------------------------------------------- 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 : 0.006 0.253 3520 Z= 0.171 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 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 187) hydrogen bonds : angle 4.84413 ( 540) covalent geometry : bond 0.00404 ( 3518) covalent geometry : angle 0.68203 ( 4801) Misc. bond : bond 0.20243 ( 2) *********************** 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 : 0.478 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: 1.0597 time to fit residues: 56.1887 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 : 0.006 0.231 3520 Z= 0.173 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 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 187) hydrogen bonds : angle 4.78891 ( 540) covalent geometry : bond 0.00411 ( 3518) covalent geometry : angle 0.66475 ( 4801) Misc. bond : bond 0.18628 ( 2) *********************** 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 : 0.382 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: 1.0464 time to fit residues: 56.5414 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 : 0.354 ------------------------------------------------------------------------------- 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 : 0.005 0.200 3520 Z= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 187) hydrogen bonds : angle 4.63404 ( 540) covalent geometry : bond 0.00332 ( 3518) covalent geometry : angle 0.61882 ( 4801) Misc. bond : bond 0.16570 ( 2) *********************** 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 : 0.345 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: 0.8046 time to fit residues: 41.3863 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 : 0.378 ------------------------------------------------------------------------------- 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: 0.0000 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: 0.9980 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: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.125494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104143 restraints weight = 3415.237| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.31 r_work: 0.3081 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 3520 Z= 0.103 Angle : 0.567 12.702 4801 Z= 0.248 Chirality : 0.039 0.139 501 Planarity : 0.003 0.039 576 Dihedral : 9.427 81.746 499 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % 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: 1.65 (0.43), residues: 397 helix: 2.08 (0.36), residues: 202 sheet: 0.15 (0.54), residues: 88 loop : 0.14 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.009 0.001 PHE A 85 TYR 0.013 0.001 TYR A 275 ARG 0.001 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 187) hydrogen bonds : angle 4.38309 ( 540) covalent geometry : bond 0.00251 ( 3518) covalent geometry : angle 0.56684 ( 4801) Misc. bond : bond 0.12812 ( 2) *********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.414 Fit side-chains REVERT: A 110 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 272 ASP cc_start: 0.8740 (p0) cc_final: 0.8530 (p0) REVERT: A 285 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7716 (tp30) outliers start: 6 outliers final: 0 residues processed: 51 average time/residue: 0.9641 time to fit residues: 51.1598 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 : 0.355 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.122714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100106 restraints weight = 3438.827| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.49 r_work: 0.3033 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 3520 Z= 0.173 Angle : 0.659 14.103 4801 Z= 0.291 Chirality : 0.042 0.145 501 Planarity : 0.003 0.041 576 Dihedral : 10.770 80.061 499 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 19.02 % 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: 1.35 (0.42), residues: 397 helix: 1.81 (0.36), residues: 202 sheet: 0.12 (0.53), residues: 88 loop : -0.02 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.008 0.001 HIS A 69 PHE 0.014 0.001 PHE A 82 TYR 0.016 0.002 TYR A 275 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 187) hydrogen bonds : angle 4.70468 ( 540) covalent geometry : bond 0.00416 ( 3518) covalent geometry : angle 0.65856 ( 4801) Misc. bond : bond 0.16603 ( 2) *********************** 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 : 0.360 Fit side-chains REVERT: A 110 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 149 ASN cc_start: 0.7950 (m-40) cc_final: 0.7558 (t0) REVERT: A 285 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: A 320 ARG cc_start: 0.7167 (mtp85) cc_final: 0.6555 (mmp80) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.9533 time to fit residues: 48.5791 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.125179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102552 restraints weight = 3375.536| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.48 r_work: 0.3069 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 3520 Z= 0.122 Angle : 0.604 13.497 4801 Z= 0.266 Chirality : 0.040 0.140 501 Planarity : 0.003 0.039 576 Dihedral : 9.948 79.848 499 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.15 % Allowed : 19.60 % 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: 1.49 (0.42), residues: 397 helix: 1.94 (0.36), residues: 202 sheet: 0.12 (0.54), residues: 88 loop : 0.06 (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 0.011 0.001 PHE A 85 TYR 0.015 0.001 TYR A 275 ARG 0.001 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 187) hydrogen bonds : angle 4.51279 ( 540) covalent geometry : bond 0.00295 ( 3518) covalent geometry : angle 0.60399 ( 4801) Misc. bond : bond 0.15123 ( 2) *********************** 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 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.410 Fit side-chains REVERT: A 110 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 186 TYR cc_start: 0.8679 (m-80) cc_final: 0.8235 (m-80) REVERT: A 272 ASP cc_start: 0.8751 (p0) cc_final: 0.8454 (p0) REVERT: A 285 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7678 (tp30) outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.8668 time to fit residues: 43.4780 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 : 0.345 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.125145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102536 restraints weight = 3414.240| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.49 r_work: 0.3069 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 3520 Z= 0.123 Angle : 0.604 13.541 4801 Z= 0.264 Chirality : 0.040 0.140 501 Planarity : 0.003 0.039 576 Dihedral : 9.864 79.394 499 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.44 % Allowed : 19.60 % 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: 1.50 (0.42), residues: 397 helix: 1.93 (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 0.007 0.001 HIS A 69 PHE 0.010 0.001 PHE A 82 TYR 0.014 0.001 TYR A 275 ARG 0.001 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 187) hydrogen bonds : angle 4.50069 ( 540) covalent geometry : bond 0.00296 ( 3518) covalent geometry : angle 0.60395 ( 4801) Misc. bond : bond 0.15076 ( 2) *********************** 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 : 0.359 Fit side-chains REVERT: A 110 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 186 TYR cc_start: 0.8669 (m-80) cc_final: 0.8221 (m-80) REVERT: A 272 ASP cc_start: 0.8754 (p0) cc_final: 0.8468 (p0) REVERT: A 285 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7665 (tp30) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.8870 time to fit residues: 45.3734 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 : 0.382 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0040 chunk 33 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.126781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104423 restraints weight = 3324.390| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.47 r_work: 0.3099 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 3520 Z= 0.106 Angle : 0.576 12.648 4801 Z= 0.252 Chirality : 0.039 0.138 501 Planarity : 0.003 0.039 576 Dihedral : 9.308 80.772 499 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.15 % Allowed : 19.31 % 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: 1.62 (0.43), residues: 397 helix: 2.05 (0.36), residues: 202 sheet: 0.15 (0.54), residues: 88 loop : 0.11 (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 0.010 0.001 PHE A 85 TYR 0.013 0.001 TYR A 275 ARG 0.001 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 187) hydrogen bonds : angle 4.35944 ( 540) covalent geometry : bond 0.00259 ( 3518) covalent geometry : angle 0.57578 ( 4801) Misc. bond : bond 0.13261 ( 2) *********************** 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 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.398 Fit side-chains REVERT: A 110 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 272 ASP cc_start: 0.8726 (p0) cc_final: 0.8511 (p0) REVERT: A 285 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7667 (tp30) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.8671 time to fit residues: 47.0682 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.125144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102651 restraints weight = 3377.986| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.48 r_work: 0.3074 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 3520 Z= 0.126 Angle : 0.615 13.749 4801 Z= 0.269 Chirality : 0.040 0.140 501 Planarity : 0.003 0.040 576 Dihedral : 9.757 78.391 499 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.44 % Allowed : 19.60 % 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: 1.52 (0.42), residues: 397 helix: 1.94 (0.36), residues: 202 sheet: 0.15 (0.54), residues: 88 loop : 0.12 (0.62), 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 85 TYR 0.014 0.002 TYR A 275 ARG 0.001 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 187) hydrogen bonds : angle 4.47309 ( 540) covalent geometry : bond 0.00305 ( 3518) covalent geometry : angle 0.61485 ( 4801) Misc. bond : bond 0.14441 ( 2) ********************** 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 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.383 Fit side-chains REVERT: A 110 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 186 TYR cc_start: 0.8626 (m-80) cc_final: 0.8253 (m-80) REVERT: A 272 ASP cc_start: 0.8757 (p0) cc_final: 0.8456 (p0) REVERT: A 285 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7675 (tp30) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.9321 time to fit residues: 47.6567 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 : 0.356 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 375 MET 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: 0.7980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.126155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103593 restraints weight = 3366.379| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.48 r_work: 0.3088 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 3520 Z= 0.114 Angle : 0.593 13.167 4801 Z= 0.260 Chirality : 0.040 0.139 501 Planarity : 0.003 0.040 576 Dihedral : 9.488 79.830 499 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.15 % Allowed : 19.60 % 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: 1.57 (0.42), residues: 397 helix: 2.00 (0.36), residues: 202 sheet: 0.13 (0.54), residues: 88 loop : 0.12 (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 0.011 0.001 PHE A 85 TYR 0.014 0.001 TYR A 275 ARG 0.000 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 187) hydrogen bonds : angle 4.40261 ( 540) covalent geometry : bond 0.00278 ( 3518) covalent geometry : angle 0.59284 ( 4801) Misc. bond : bond 0.13442 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.37 seconds wall clock time: 50 minutes 34.44 seconds (3034.44 seconds total)