Starting phenix.real_space_refine on Fri May 9 16:24:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.map" model { file = "/net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9joz_61690/05_2025/9joz_61690.cif" } resolution = 2.94 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= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2104 2.51 5 N 515 2.21 5 O 514 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: 3143 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain breaks: 2 Time building chain proxies: 2.72, per 1000 atoms: 0.87 Number of scatterers: 3143 At special positions: 0 Unit cell: (68, 65, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 514 8.00 N 515 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 368.1 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.569A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.696A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.861A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.280A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.508A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.391A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 264 through 294 removed outlier: 3.512A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.671A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 390 Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 419 Processing helix chain 'A' and resid 427 through 456 240 hydrogen bonds defined for protein. 720 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: 0.92 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 929 1.34 - 1.46: 799 1.46 - 1.58: 1487 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3231 Sorted by residual: bond pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" N LYS A 393 " pdb=" CA LYS A 393 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" CA SER A 138 " pdb=" CB SER A 138 " ideal model delta sigma weight residual 1.532 1.494 0.039 1.53e-02 4.27e+03 6.48e+00 bond pdb=" N SER A 73 " pdb=" CA SER A 73 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.80e+00 bond pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.74e+00 ... (remaining 3226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 4217 1.07 - 2.13: 122 2.13 - 3.20: 49 3.20 - 4.27: 5 4.27 - 5.33: 6 Bond angle restraints: 4399 Sorted by residual: angle pdb=" N SER A 138 " pdb=" CA SER A 138 " pdb=" C SER A 138 " ideal model delta sigma weight residual 113.41 109.79 3.62 1.22e+00 6.72e-01 8.82e+00 angle pdb=" C PHE A 385 " pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " ideal model delta sigma weight residual 110.85 115.51 -4.66 1.70e+00 3.46e-01 7.50e+00 angle pdb=" CA PHE A 385 " pdb=" CB PHE A 385 " pdb=" CG PHE A 385 " ideal model delta sigma weight residual 113.80 116.43 -2.63 1.00e+00 1.00e+00 6.93e+00 angle pdb=" CA LYS A 393 " pdb=" C LYS A 393 " pdb=" O LYS A 393 " ideal model delta sigma weight residual 120.89 118.02 2.87 1.10e+00 8.26e-01 6.80e+00 angle pdb=" O SER A 313 " pdb=" C SER A 313 " pdb=" N THR A 314 " ideal model delta sigma weight residual 122.07 124.68 -2.61 1.03e+00 9.43e-01 6.42e+00 ... (remaining 4394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1598 17.01 - 34.02: 187 34.02 - 51.03: 45 51.03 - 68.05: 15 68.05 - 85.06: 5 Dihedral angle restraints: 1850 sinusoidal: 702 harmonic: 1148 Sorted by residual: dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N VAL A 144 " pdb=" CA VAL A 144 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 -163.42 -16.58 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 85.06 -85.06 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 1847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 408 0.047 - 0.094: 90 0.094 - 0.141: 11 0.141 - 0.188: 3 0.188 - 0.235: 1 Chirality restraints: 513 Sorted by residual: chirality pdb=" CB VAL A 144 " pdb=" CA VAL A 144 " pdb=" CG1 VAL A 144 " pdb=" CG2 VAL A 144 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 140 " pdb=" CA ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CG2 ILE A 140 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 510 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 303 " -0.262 9.50e-02 1.11e+02 1.17e-01 8.45e+00 pdb=" NE ARG A 303 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 303 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 303 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 303 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 70 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 145 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 146 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.022 5.00e-02 4.00e+02 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 985 2.82 - 3.34: 3149 3.34 - 3.86: 5608 3.86 - 4.38: 6478 4.38 - 4.90: 10914 Nonbonded interactions: 27134 Sorted by model distance: nonbonded pdb=" O ILE A 339 " pdb=" OG1 THR A 343 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O GLN A 377 " model vdw 2.300 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.342 3.040 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.342 3.040 ... (remaining 27129 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: 0.690 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: 12.480 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3231 Z= 0.199 Angle : 0.514 5.334 4399 Z= 0.312 Chirality : 0.040 0.235 513 Planarity : 0.007 0.117 526 Dihedral : 16.758 85.057 1112 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.89 % Allowed : 23.81 % Favored : 75.30 % 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 (0.43), residues: 384 helix: 1.57 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.53 (0.71), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 457 PHE 0.013 0.001 PHE A 84 TYR 0.010 0.001 TYR A 438 ARG 0.007 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.10672 ( 240) hydrogen bonds : angle 4.91020 ( 720) covalent geometry : bond 0.00309 ( 3231) covalent geometry : angle 0.51410 ( 4399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.341 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 1.0025 time to fit residues: 35.5014 Evaluate side-chains 31 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 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 = 0.3689 r_free = 0.3689 target = 0.152123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115473 restraints weight = 3335.242| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.03 r_work: 0.2992 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3231 Z= 0.171 Angle : 0.502 5.552 4399 Z= 0.266 Chirality : 0.040 0.169 513 Planarity : 0.005 0.058 526 Dihedral : 5.450 59.832 439 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.27 % Allowed : 22.92 % Favored : 73.81 % 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: 1.69 (0.43), residues: 384 helix: 1.76 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.17 (0.72), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.023 0.002 PHE A 84 TYR 0.015 0.001 TYR A 35 ARG 0.006 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 240) hydrogen bonds : angle 3.92521 ( 720) covalent geometry : bond 0.00402 ( 3231) covalent geometry : angle 0.50160 ( 4399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.350 Fit side-chains REVERT: A 30 CYS cc_start: 0.8938 (m) cc_final: 0.8701 (m) REVERT: A 263 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7094 (ttm-80) outliers start: 11 outliers final: 4 residues processed: 37 average time/residue: 1.0863 time to fit residues: 41.6974 Evaluate side-chains 32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.0010 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117409 restraints weight = 3249.025| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.02 r_work: 0.3031 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3231 Z= 0.123 Angle : 0.458 5.324 4399 Z= 0.242 Chirality : 0.038 0.154 513 Planarity : 0.005 0.058 526 Dihedral : 4.712 58.723 437 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.79 % Allowed : 23.81 % Favored : 74.40 % 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: 1.96 (0.44), residues: 384 helix: 1.98 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.21 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.004 0.001 HIS A 457 PHE 0.017 0.001 PHE A 84 TYR 0.010 0.001 TYR A 139 ARG 0.007 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 240) hydrogen bonds : angle 3.72954 ( 720) covalent geometry : bond 0.00271 ( 3231) covalent geometry : angle 0.45794 ( 4399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.341 Fit side-chains REVERT: A 262 LEU cc_start: 0.7563 (tp) cc_final: 0.7197 (mm) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.9312 time to fit residues: 32.1223 Evaluate side-chains 31 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.147786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110517 restraints weight = 3337.955| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.07 r_work: 0.3015 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3231 Z= 0.156 Angle : 0.481 5.454 4399 Z= 0.255 Chirality : 0.039 0.129 513 Planarity : 0.005 0.056 526 Dihedral : 4.705 56.185 437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.98 % Allowed : 22.62 % Favored : 74.40 % 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: 1.92 (0.44), residues: 384 helix: 1.93 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.15 (0.74), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.022 0.002 PHE A 84 TYR 0.014 0.001 TYR A 35 ARG 0.007 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 240) hydrogen bonds : angle 3.77953 ( 720) covalent geometry : bond 0.00362 ( 3231) covalent geometry : angle 0.48148 ( 4399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.358 Fit side-chains REVERT: A 25 TRP cc_start: 0.6171 (p90) cc_final: 0.5891 (p90) REVERT: A 59 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: A 263 ARG cc_start: 0.7656 (tpt90) cc_final: 0.7090 (tpp-160) outliers start: 10 outliers final: 4 residues processed: 37 average time/residue: 1.0497 time to fit residues: 40.4072 Evaluate side-chains 34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.163286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127271 restraints weight = 3328.511| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.04 r_work: 0.3035 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3231 Z= 0.142 Angle : 0.475 5.448 4399 Z= 0.249 Chirality : 0.038 0.125 513 Planarity : 0.005 0.056 526 Dihedral : 4.639 54.841 437 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.27 % Allowed : 22.62 % Favored : 74.11 % 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: 1.96 (0.44), residues: 384 helix: 2.00 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.32 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.004 0.001 HIS A 457 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.008 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 240) hydrogen bonds : angle 3.72811 ( 720) covalent geometry : bond 0.00327 ( 3231) covalent geometry : angle 0.47475 ( 4399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.329 Fit side-chains REVERT: A 59 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: A 262 LEU cc_start: 0.7344 (tp) cc_final: 0.7098 (mm) REVERT: A 263 ARG cc_start: 0.7773 (tpt90) cc_final: 0.7258 (ttm-80) REVERT: A 456 ARG cc_start: 0.7299 (ptp-110) cc_final: 0.6470 (ttp80) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 1.0434 time to fit residues: 41.0797 Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.148654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111389 restraints weight = 3330.977| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.05 r_work: 0.3015 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3231 Z= 0.134 Angle : 0.467 5.456 4399 Z= 0.246 Chirality : 0.038 0.125 513 Planarity : 0.005 0.055 526 Dihedral : 4.576 53.219 437 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.27 % Allowed : 23.51 % Favored : 73.21 % 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: 1.99 (0.44), residues: 384 helix: 2.01 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.29 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.019 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.007 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 240) hydrogen bonds : angle 3.68618 ( 720) covalent geometry : bond 0.00304 ( 3231) covalent geometry : angle 0.46730 ( 4399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.433 Fit side-chains REVERT: A 262 LEU cc_start: 0.7341 (tp) cc_final: 0.7095 (mm) REVERT: A 456 ARG cc_start: 0.7225 (ptp-110) cc_final: 0.6407 (ttp80) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.9649 time to fit residues: 35.2066 Evaluate side-chains 34 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 33 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 = 0.3820 r_free = 0.3820 target = 0.162260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126614 restraints weight = 3280.853| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.00 r_work: 0.2993 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3231 Z= 0.158 Angle : 0.484 5.470 4399 Z= 0.256 Chirality : 0.038 0.127 513 Planarity : 0.005 0.054 526 Dihedral : 4.597 51.719 437 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.27 % Allowed : 23.81 % Favored : 72.92 % 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: 1.96 (0.44), residues: 384 helix: 1.98 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.22 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.000 HIS A 457 PHE 0.022 0.001 PHE A 84 TYR 0.014 0.001 TYR A 35 ARG 0.009 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 240) hydrogen bonds : angle 3.74922 ( 720) covalent geometry : bond 0.00368 ( 3231) covalent geometry : angle 0.48439 ( 4399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.346 Fit side-chains REVERT: A 26 ARG cc_start: 0.5213 (ptm160) cc_final: 0.4806 (ptm160) REVERT: A 263 ARG cc_start: 0.7634 (tpt90) cc_final: 0.7108 (tpp-160) REVERT: A 456 ARG cc_start: 0.7254 (ptp-110) cc_final: 0.6467 (ttp80) outliers start: 11 outliers final: 6 residues processed: 35 average time/residue: 1.0634 time to fit residues: 38.6745 Evaluate side-chains 33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111722 restraints weight = 3323.085| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.04 r_work: 0.3029 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3231 Z= 0.130 Angle : 0.467 5.475 4399 Z= 0.246 Chirality : 0.038 0.131 513 Planarity : 0.005 0.055 526 Dihedral : 4.528 51.168 437 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.98 % Allowed : 25.00 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.44), residues: 384 helix: 2.05 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.36 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS A 457 PHE 0.018 0.001 PHE A 84 TYR 0.012 0.001 TYR A 139 ARG 0.008 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 240) hydrogen bonds : angle 3.66507 ( 720) covalent geometry : bond 0.00293 ( 3231) covalent geometry : angle 0.46654 ( 4399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.314 Fit side-chains REVERT: A 26 ARG cc_start: 0.5144 (ptm160) cc_final: 0.4670 (ptm160) REVERT: A 262 LEU cc_start: 0.7303 (tp) cc_final: 0.7050 (mm) REVERT: A 456 ARG cc_start: 0.7097 (ptp-110) cc_final: 0.6413 (ttp80) outliers start: 10 outliers final: 8 residues processed: 33 average time/residue: 1.0096 time to fit residues: 34.6866 Evaluate side-chains 35 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.148107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111098 restraints weight = 3323.267| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.03 r_work: 0.2991 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3231 Z= 0.155 Angle : 0.486 5.479 4399 Z= 0.257 Chirality : 0.038 0.129 513 Planarity : 0.005 0.054 526 Dihedral : 4.551 49.924 437 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.98 % Allowed : 24.70 % Favored : 72.32 % 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: 1.96 (0.44), residues: 384 helix: 1.99 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.25 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.000 HIS A 457 PHE 0.022 0.001 PHE A 84 TYR 0.014 0.001 TYR A 35 ARG 0.009 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 240) hydrogen bonds : angle 3.72946 ( 720) covalent geometry : bond 0.00359 ( 3231) covalent geometry : angle 0.48621 ( 4399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.371 Fit side-chains REVERT: A 26 ARG cc_start: 0.5113 (ptm160) cc_final: 0.4628 (ptm160) REVERT: A 263 ARG cc_start: 0.7618 (tpt90) cc_final: 0.7052 (ttm-80) REVERT: A 456 ARG cc_start: 0.7116 (ptp-110) cc_final: 0.6437 (ttp80) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 1.0794 time to fit residues: 39.1547 Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 457 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115838 restraints weight = 3250.075| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.03 r_work: 0.3024 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3231 Z= 0.123 Angle : 0.466 5.431 4399 Z= 0.246 Chirality : 0.037 0.133 513 Planarity : 0.005 0.055 526 Dihedral : 4.494 49.734 437 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.98 % Allowed : 24.40 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.44), residues: 384 helix: 2.08 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.21 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 457 PHE 0.017 0.001 PHE A 84 TYR 0.011 0.001 TYR A 139 ARG 0.009 0.001 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 240) hydrogen bonds : angle 3.65101 ( 720) covalent geometry : bond 0.00270 ( 3231) covalent geometry : angle 0.46579 ( 4399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.332 Fit side-chains REVERT: A 262 LEU cc_start: 0.7282 (tp) cc_final: 0.7026 (mm) REVERT: A 456 ARG cc_start: 0.7094 (ptp-110) cc_final: 0.6478 (ttp80) outliers start: 10 outliers final: 8 residues processed: 36 average time/residue: 0.8556 time to fit residues: 32.1893 Evaluate side-chains 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 457 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112413 restraints weight = 3305.353| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.06 r_work: 0.3045 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3231 Z= 0.136 Angle : 0.471 5.467 4399 Z= 0.249 Chirality : 0.038 0.133 513 Planarity : 0.005 0.056 526 Dihedral : 4.486 49.246 437 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.68 % Allowed : 24.70 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.44), residues: 384 helix: 2.06 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -2.24 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 457 PHE 0.019 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 240) hydrogen bonds : angle 3.66908 ( 720) covalent geometry : bond 0.00308 ( 3231) covalent geometry : angle 0.47137 ( 4399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.49 seconds wall clock time: 42 minutes 27.63 seconds (2547.63 seconds total)