Starting phenix.real_space_refine on Wed Mar 5 23:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9w_51159/03_2025/9g9w_51159.cif" } resolution = 2.48 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= 0.048 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 32 5.16 5 C 2732 2.51 5 N 616 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4089 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1938 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 253} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 108 Unusual residues: {' K': 3, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B Time building chain proxies: 3.80, per 1000 atoms: 0.93 Number of scatterers: 4089 At special positions: 0 Unit cell: (60.736, 80.704, 94.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 32 16.00 O 706 8.00 N 616 7.00 C 2732 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: 1.22 Conformation dependent library (CDL) restraints added in 484.1 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.573A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 3.979A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.573A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 3.980A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.675A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 248 removed outlier: 5.290A pdb=" N ARG B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 343 hydrogen bonds defined for protein. 1029 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: 1.14 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 632 1.32 - 1.44: 1134 1.44 - 1.56: 2376 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 4192 Sorted by residual: bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.513 0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CAL Y01 B 302 " pdb=" CAX Y01 B 302 " ideal model delta sigma weight residual 1.540 1.514 0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" CAL Y01 B 303 " pdb=" CAX Y01 B 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 A 303 " pdb=" CAX Y01 A 303 " ideal model delta sigma weight residual 1.540 1.515 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CAL Y01 B 301 " pdb=" CAX Y01 B 301 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 4187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 4931 0.95 - 1.90: 653 1.90 - 2.86: 94 2.86 - 3.81: 34 3.81 - 4.76: 18 Bond angle restraints: 5730 Sorted by residual: angle pdb=" N SER B 31 " pdb=" CA SER B 31 " pdb=" C SER B 31 " ideal model delta sigma weight residual 111.82 115.38 -3.56 1.16e+00 7.43e-01 9.41e+00 angle pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" C SER A 31 " ideal model delta sigma weight residual 111.82 115.34 -3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA TYR A 96 " pdb=" CB TYR A 96 " pdb=" CG TYR A 96 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CA TYR B 96 " pdb=" CB TYR B 96 " pdb=" CG TYR B 96 " ideal model delta sigma weight residual 113.90 117.99 -4.09 1.80e+00 3.09e-01 5.16e+00 angle pdb=" N PHE A 80 " pdb=" CA PHE A 80 " pdb=" C PHE A 80 " ideal model delta sigma weight residual 111.11 113.66 -2.55 1.20e+00 6.94e-01 4.53e+00 ... (remaining 5725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2486 15.06 - 30.13: 160 30.13 - 45.19: 34 45.19 - 60.25: 20 60.25 - 75.31: 2 Dihedral angle restraints: 2702 sinusoidal: 1202 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 341 0.034 - 0.068: 253 0.068 - 0.103: 60 0.103 - 0.137: 22 0.137 - 0.171: 6 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA TRP B 78 " pdb=" N TRP B 78 " pdb=" C TRP B 78 " pdb=" CB TRP B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 679 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG B 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.73e+00 pdb=" C ARG A 137 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 138 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 39 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C GLU A 39 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 39 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 40 " -0.012 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 1394 2.86 - 3.43: 4737 3.43 - 4.00: 7582 4.00 - 4.57: 11233 4.57 - 5.14: 15661 Nonbonded interactions: 40607 Sorted by model distance: nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU B 182 " pdb=" OH TYR B 220 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.420 3.040 ... (remaining 40602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 259 or resid 301 through 303)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 0.007 0.044 4192 Z= 0.468 Angle : 0.724 4.758 5730 Z= 0.446 Chirality : 0.050 0.171 682 Planarity : 0.006 0.022 680 Dihedral : 11.378 75.314 1742 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.55 (0.33), residues: 512 helix: 0.52 (0.22), residues: 420 sheet: None (None), residues: 0 loop : 0.25 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 78 HIS 0.003 0.001 HIS B 188 PHE 0.026 0.002 PHE B 202 TYR 0.022 0.005 TYR A 96 ARG 0.004 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.436 Fit side-chains REVERT: A 3 ARG cc_start: 0.5993 (ttt180) cc_final: 0.5750 (ttt-90) REVERT: A 47 ARG cc_start: 0.6227 (ttt-90) cc_final: 0.5936 (ttp80) REVERT: A 135 PHE cc_start: 0.7716 (t80) cc_final: 0.7422 (t80) REVERT: A 137 ARG cc_start: 0.6533 (ttm-80) cc_final: 0.6138 (ttp-170) REVERT: B 3 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5762 (ttt-90) REVERT: B 47 ARG cc_start: 0.6222 (ttt-90) cc_final: 0.5931 (ttp80) REVERT: B 135 PHE cc_start: 0.7738 (t80) cc_final: 0.7445 (t80) REVERT: B 137 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6154 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.2671 time to fit residues: 89.0622 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104277 restraints weight = 4576.784| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.66 r_work: 0.2963 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4192 Z= 0.152 Angle : 0.428 4.809 5730 Z= 0.238 Chirality : 0.037 0.126 682 Planarity : 0.003 0.029 680 Dihedral : 7.399 52.869 978 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.12 % 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: 3.82 (0.35), residues: 512 helix: 2.93 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.52 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 78 HIS 0.001 0.000 HIS A 188 PHE 0.016 0.001 PHE A 109 TYR 0.012 0.002 TYR A 96 ARG 0.001 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.401 Fit side-chains REVERT: A 3 ARG cc_start: 0.6257 (ttt180) cc_final: 0.5971 (ttt-90) REVERT: A 135 PHE cc_start: 0.7863 (t80) cc_final: 0.7523 (t80) REVERT: A 137 ARG cc_start: 0.6314 (ttm-80) cc_final: 0.6012 (ttp-170) REVERT: B 3 ARG cc_start: 0.6257 (ttt180) cc_final: 0.5981 (ttt-90) REVERT: B 135 PHE cc_start: 0.7866 (t80) cc_final: 0.7525 (t80) REVERT: B 137 ARG cc_start: 0.6313 (ttm-80) cc_final: 0.6013 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 62 average time/residue: 1.6350 time to fit residues: 104.1802 Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099761 restraints weight = 4539.847| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.68 r_work: 0.3116 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4192 Z= 0.272 Angle : 0.475 5.035 5730 Z= 0.262 Chirality : 0.039 0.140 682 Planarity : 0.003 0.027 680 Dihedral : 7.278 52.160 978 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.26 % Allowed : 9.26 % Favored : 90.48 % 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: 4.05 (0.35), residues: 512 helix: 3.17 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.14 (0.66), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 78 HIS 0.001 0.000 HIS A 72 PHE 0.017 0.002 PHE A 109 TYR 0.015 0.002 TYR A 96 ARG 0.001 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.398 Fit side-chains REVERT: A 3 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6177 (ttt-90) REVERT: A 51 LYS cc_start: 0.6863 (tttt) cc_final: 0.6598 (tttt) REVERT: A 135 PHE cc_start: 0.8010 (t80) cc_final: 0.7714 (t80) REVERT: A 137 ARG cc_start: 0.6539 (ttm-80) cc_final: 0.6171 (ttp-170) REVERT: B 3 ARG cc_start: 0.6511 (ttt180) cc_final: 0.6135 (ttt-90) REVERT: B 51 LYS cc_start: 0.6852 (tttt) cc_final: 0.6588 (tttt) REVERT: B 135 PHE cc_start: 0.8010 (t80) cc_final: 0.7713 (t80) REVERT: B 137 ARG cc_start: 0.6544 (ttm-80) cc_final: 0.6174 (ttp-170) outliers start: 1 outliers final: 2 residues processed: 66 average time/residue: 1.5996 time to fit residues: 108.4237 Evaluate side-chains 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101548 restraints weight = 4588.728| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.65 r_work: 0.2951 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4192 Z= 0.184 Angle : 0.415 5.056 5730 Z= 0.230 Chirality : 0.036 0.127 682 Planarity : 0.002 0.024 680 Dihedral : 7.043 53.875 978 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.61 (0.36), residues: 512 helix: 3.52 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.84 (0.71), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 78 HIS 0.001 0.000 HIS A 33 PHE 0.015 0.001 PHE A 109 TYR 0.012 0.001 TYR A 96 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.399 Fit side-chains REVERT: A 3 ARG cc_start: 0.6329 (ttt180) cc_final: 0.5993 (ttt-90) REVERT: A 135 PHE cc_start: 0.7814 (t80) cc_final: 0.7512 (t80) REVERT: A 137 ARG cc_start: 0.6266 (ttm-80) cc_final: 0.5935 (ttp-170) REVERT: B 3 ARG cc_start: 0.6348 (ttt180) cc_final: 0.6007 (ttt-90) REVERT: B 135 PHE cc_start: 0.7813 (t80) cc_final: 0.7509 (t80) REVERT: B 137 ARG cc_start: 0.6249 (ttm-80) cc_final: 0.5921 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.5170 time to fit residues: 96.7188 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099549 restraints weight = 4693.562| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.66 r_work: 0.2919 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4192 Z= 0.250 Angle : 0.451 5.122 5730 Z= 0.248 Chirality : 0.038 0.136 682 Planarity : 0.002 0.024 680 Dihedral : 7.082 54.713 978 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % 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: 4.50 (0.36), residues: 512 helix: 3.45 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.78 (0.71), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.015 0.002 PHE B 109 TYR 0.013 0.002 TYR A 96 ARG 0.001 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.466 Fit side-chains REVERT: A 3 ARG cc_start: 0.6407 (ttt180) cc_final: 0.6072 (ttt-90) REVERT: A 135 PHE cc_start: 0.7826 (t80) cc_final: 0.7535 (t80) REVERT: A 137 ARG cc_start: 0.6274 (ttm-80) cc_final: 0.5927 (ttp-170) REVERT: B 3 ARG cc_start: 0.6424 (ttt180) cc_final: 0.6090 (ttt-90) REVERT: B 135 PHE cc_start: 0.7827 (t80) cc_final: 0.7535 (t80) REVERT: B 137 ARG cc_start: 0.6262 (ttm-80) cc_final: 0.5920 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.8593 time to fit residues: 118.2921 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101866 restraints weight = 4524.124| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.66 r_work: 0.2938 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4192 Z= 0.206 Angle : 0.425 5.129 5730 Z= 0.234 Chirality : 0.036 0.129 682 Planarity : 0.002 0.023 680 Dihedral : 6.971 56.163 978 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.60 (0.36), residues: 512 helix: 3.53 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.73 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.015 0.001 PHE A 109 TYR 0.011 0.001 TYR A 96 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.399 Fit side-chains REVERT: A 3 ARG cc_start: 0.6377 (ttt180) cc_final: 0.5988 (ttt-90) REVERT: A 47 ARG cc_start: 0.6465 (ttt-90) cc_final: 0.5993 (ttp80) REVERT: A 135 PHE cc_start: 0.7819 (t80) cc_final: 0.7540 (t80) REVERT: A 137 ARG cc_start: 0.6264 (ttm-80) cc_final: 0.5918 (ttp-170) REVERT: B 3 ARG cc_start: 0.6386 (ttt180) cc_final: 0.6058 (ttt-90) REVERT: B 47 ARG cc_start: 0.6452 (ttt-90) cc_final: 0.5985 (ttp80) REVERT: B 135 PHE cc_start: 0.7820 (t80) cc_final: 0.7540 (t80) REVERT: B 137 ARG cc_start: 0.6258 (ttm-80) cc_final: 0.5914 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 1.5665 time to fit residues: 99.7266 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100144 restraints weight = 4639.065| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.66 r_work: 0.2925 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4192 Z= 0.229 Angle : 0.442 5.150 5730 Z= 0.242 Chirality : 0.037 0.133 682 Planarity : 0.002 0.022 680 Dihedral : 7.015 57.281 978 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.53 % Allowed : 11.64 % Favored : 87.83 % 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: 4.51 (0.36), residues: 512 helix: 3.48 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.67 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.015 0.001 PHE A 109 TYR 0.011 0.001 TYR B 96 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.420 Fit side-chains REVERT: A 3 ARG cc_start: 0.6386 (ttt180) cc_final: 0.6000 (ttt-90) REVERT: A 47 ARG cc_start: 0.6647 (ttt-90) cc_final: 0.6141 (ttp80) REVERT: A 135 PHE cc_start: 0.7813 (t80) cc_final: 0.7547 (t80) REVERT: A 137 ARG cc_start: 0.6261 (ttm-80) cc_final: 0.5913 (ttp-170) REVERT: B 3 ARG cc_start: 0.6420 (ttt180) cc_final: 0.6096 (ttt-90) REVERT: B 47 ARG cc_start: 0.6638 (ttt-90) cc_final: 0.6136 (ttp80) REVERT: B 135 PHE cc_start: 0.7812 (t80) cc_final: 0.7547 (t80) REVERT: B 137 ARG cc_start: 0.6255 (ttm-80) cc_final: 0.5909 (ttp-170) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 1.6904 time to fit residues: 107.5147 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104724 restraints weight = 4362.783| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.62 r_work: 0.2981 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4192 Z= 0.145 Angle : 0.391 5.085 5730 Z= 0.214 Chirality : 0.035 0.120 682 Planarity : 0.002 0.021 680 Dihedral : 6.761 59.945 978 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.79 (0.36), residues: 512 helix: 3.66 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.74 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.000 0.000 HIS A 98 PHE 0.014 0.001 PHE A 109 TYR 0.010 0.001 TYR A 96 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.431 Fit side-chains REVERT: A 3 ARG cc_start: 0.6294 (ttt180) cc_final: 0.5916 (ttt-90) REVERT: A 47 ARG cc_start: 0.6642 (ttt-90) cc_final: 0.6103 (ttp80) REVERT: A 135 PHE cc_start: 0.7789 (t80) cc_final: 0.7451 (t80) REVERT: A 137 ARG cc_start: 0.6189 (ttm-80) cc_final: 0.5854 (ttp-170) REVERT: B 3 ARG cc_start: 0.6342 (ttt180) cc_final: 0.6019 (ttt-90) REVERT: B 47 ARG cc_start: 0.6638 (ttt-90) cc_final: 0.6102 (ttp80) REVERT: B 135 PHE cc_start: 0.7784 (t80) cc_final: 0.7453 (t80) REVERT: B 137 ARG cc_start: 0.6186 (ttm-80) cc_final: 0.5852 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 2.1845 time to fit residues: 125.4014 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102812 restraints weight = 4479.396| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.64 r_work: 0.2954 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4192 Z= 0.184 Angle : 0.415 5.131 5730 Z= 0.226 Chirality : 0.036 0.127 682 Planarity : 0.002 0.021 680 Dihedral : 6.759 58.692 978 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.75 (0.36), residues: 512 helix: 3.61 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.85 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.000 0.000 HIS B 98 PHE 0.014 0.001 PHE A 109 TYR 0.010 0.001 TYR A 96 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.528 Fit side-chains REVERT: A 3 ARG cc_start: 0.6285 (ttt180) cc_final: 0.5905 (ttt-90) REVERT: A 135 PHE cc_start: 0.7785 (t80) cc_final: 0.7454 (t80) REVERT: A 137 ARG cc_start: 0.6130 (ttm-80) cc_final: 0.5787 (ttp-170) REVERT: B 3 ARG cc_start: 0.6332 (ttt180) cc_final: 0.6005 (ttt-90) REVERT: B 135 PHE cc_start: 0.7788 (t80) cc_final: 0.7457 (t80) REVERT: B 137 ARG cc_start: 0.6122 (ttm-80) cc_final: 0.5780 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 2.0609 time to fit residues: 131.4449 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102895 restraints weight = 4532.803| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.65 r_work: 0.2955 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4192 Z= 0.179 Angle : 0.414 5.129 5730 Z= 0.226 Chirality : 0.035 0.125 682 Planarity : 0.002 0.021 680 Dihedral : 6.726 57.642 978 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % 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: 4.76 (0.36), residues: 512 helix: 3.62 (0.23), residues: 414 sheet: None (None), residues: 0 loop : 0.84 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 PHE 0.014 0.001 PHE B 109 TYR 0.010 0.001 TYR A 96 ARG 0.002 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.452 Fit side-chains REVERT: A 3 ARG cc_start: 0.6348 (ttt180) cc_final: 0.5967 (ttt-90) REVERT: A 135 PHE cc_start: 0.7848 (t80) cc_final: 0.7513 (t80) REVERT: A 137 ARG cc_start: 0.6206 (ttm-80) cc_final: 0.5853 (ttp-170) REVERT: B 3 ARG cc_start: 0.6399 (ttt180) cc_final: 0.6071 (ttt-90) REVERT: B 135 PHE cc_start: 0.7850 (t80) cc_final: 0.7515 (t80) REVERT: B 137 ARG cc_start: 0.6195 (ttm-80) cc_final: 0.5845 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 62 average time/residue: 2.2387 time to fit residues: 142.7150 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100073 restraints weight = 4486.196| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.64 r_work: 0.2908 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4192 Z= 0.297 Angle : 0.489 5.205 5730 Z= 0.264 Chirality : 0.039 0.141 682 Planarity : 0.002 0.022 680 Dihedral : 7.179 59.205 978 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % 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: 4.49 (0.36), residues: 512 helix: 3.45 (0.23), residues: 412 sheet: None (None), residues: 0 loop : 0.75 (0.67), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.015 0.002 PHE A 109 TYR 0.012 0.002 TYR A 96 ARG 0.003 0.001 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.83 seconds wall clock time: 74 minutes 47.08 seconds (4487.08 seconds total)