Starting phenix.real_space_refine on Thu Mar 6 08:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2s_43757/03_2025/8w2s_43757.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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 P 137 5.49 5 S 11 5.16 5 C 3025 2.51 5 N 1051 2.21 5 O 1464 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: 5688 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2761 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2927 Classifications: {'RNA': 137} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 55} Link IDs: {'rna2p': 13, 'rna3p': 123} Time building chain proxies: 4.16, per 1000 atoms: 0.73 Number of scatterers: 5688 At special positions: 0 Unit cell: (86.6528, 86.6528, 115.815, 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) S 11 16.00 P 137 15.00 O 1464 8.00 N 1051 7.00 C 3025 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: 1.28 Conformation dependent library (CDL) restraints added in 482.3 milliseconds 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 56.0% alpha, 5.3% beta 50 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 75 removed outlier: 3.690A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.836A pdb=" N GLU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.665A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.521A pdb=" N ASP A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.518A pdb=" N ARG A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.617A pdb=" N ILE A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 removed outlier: 4.166A pdb=" N GLU A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 583 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 608 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643 removed outlier: 3.569A pdb=" N ILE A 641 " --> pdb=" O PHE A 648 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1109 1.33 - 1.45: 2107 1.45 - 1.57: 2567 1.57 - 1.69: 273 1.69 - 1.81: 16 Bond restraints: 6072 Sorted by residual: bond pdb=" CB GLU A 107 " pdb=" CG GLU A 107 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" C3' U B 92 " pdb=" O3' U B 92 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.51e+00 bond pdb=" CG1 ILE A 252 " pdb=" CD1 ILE A 252 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.31e+00 bond pdb=" CB LYS A 124 " pdb=" CG LYS A 124 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 1.607 1.627 -0.020 1.50e-02 4.44e+03 1.82e+00 ... (remaining 6067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 8670 2.69 - 5.37: 130 5.37 - 8.06: 27 8.06 - 10.74: 6 10.74 - 13.43: 4 Bond angle restraints: 8837 Sorted by residual: angle pdb=" N LYS A 172 " pdb=" CA LYS A 172 " pdb=" C LYS A 172 " ideal model delta sigma weight residual 108.67 95.45 13.22 1.55e+00 4.16e-01 7.27e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 111.33 120.20 -8.87 1.21e+00 6.83e-01 5.38e+01 angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 124.83 -10.83 1.50e+00 4.44e-01 5.21e+01 angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 117.21 -9.01 1.50e+00 4.44e-01 3.61e+01 angle pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" C THR A 261 " ideal model delta sigma weight residual 108.63 99.71 8.92 1.60e+00 3.91e-01 3.10e+01 ... (remaining 8832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 3552 35.33 - 70.66: 282 70.66 - 105.99: 33 105.99 - 141.32: 1 141.32 - 176.65: 2 Dihedral angle restraints: 3870 sinusoidal: 2874 harmonic: 996 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 48.65 -176.65 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 181 " pdb=" C LYS A 181 " pdb=" N CYS A 182 " pdb=" CA CYS A 182 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual 254.00 176.43 77.57 1 1.70e+01 3.46e-03 2.61e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 1085 0.175 - 0.350: 3 0.350 - 0.524: 0 0.524 - 0.699: 0 0.699 - 0.874: 1 Chirality restraints: 1089 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' G B 122 " pdb=" C4' G B 122 " pdb=" O3' G B 122 " pdb=" C2' G B 122 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1086 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " 0.066 2.00e-02 2.50e+03 3.07e-02 2.82e+01 pdb=" N9 G B 142 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 142 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 142 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G B 142 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 142 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 142 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ARG A 137 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 138 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 173 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ARG A 173 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 173 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 174 " -0.011 2.00e-02 2.50e+03 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1441 2.81 - 3.33: 5025 3.33 - 3.86: 11190 3.86 - 4.38: 12754 4.38 - 4.90: 17411 Nonbonded interactions: 47821 Sorted by model distance: nonbonded pdb=" O2' G B 11 " pdb=" O4' A B 12 " model vdw 2.289 3.040 nonbonded pdb=" OP2 U B 91 " pdb=" O2' U B 92 " model vdw 2.296 3.040 nonbonded pdb=" O PRO A 558 " pdb=" O2' U B 22 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU A 212 " pdb=" OG SER A 214 " model vdw 2.322 3.040 nonbonded pdb=" N2 G B 117 " pdb=" OP2 A B 120 " model vdw 2.340 3.120 ... (remaining 47816 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 ========== 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: 2.520 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 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: 0.8012 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6072 Z= 0.242 Angle : 0.889 13.428 8837 Z= 0.484 Chirality : 0.049 0.874 1089 Planarity : 0.005 0.048 621 Dihedral : 20.847 176.648 3218 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.44), residues: 331 helix: -0.51 (0.37), residues: 170 sheet: 1.34 (1.12), residues: 10 loop : -1.46 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 127 HIS 0.008 0.002 HIS A 267 PHE 0.016 0.002 PHE A 236 TYR 0.021 0.003 TYR A 97 ARG 0.006 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.426 Fit side-chains REVERT: A 124 LYS cc_start: 0.8091 (tppt) cc_final: 0.7772 (mtpt) REVERT: A 248 GLN cc_start: 0.9077 (mt0) cc_final: 0.8659 (mp10) REVERT: A 579 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7958 (mtpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2522 time to fit residues: 16.0767 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.146705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102019 restraints weight = 11805.804| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.12 r_work: 0.3345 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6072 Z= 0.213 Angle : 0.619 9.888 8837 Z= 0.337 Chirality : 0.042 0.697 1089 Planarity : 0.004 0.032 621 Dihedral : 21.707 166.975 2488 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.07 % Allowed : 11.95 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.48), residues: 331 helix: 0.71 (0.40), residues: 174 sheet: 1.16 (1.18), residues: 10 loop : -1.23 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.003 0.001 HIS A 91 PHE 0.014 0.001 PHE A 570 TYR 0.017 0.002 TYR A 97 ARG 0.004 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.413 Fit side-chains REVERT: A 248 GLN cc_start: 0.9065 (mt0) cc_final: 0.8580 (mp10) REVERT: A 579 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8228 (mtpp) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.2470 time to fit residues: 16.0976 Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 645 ASN A 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.145403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101146 restraints weight = 11671.822| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.06 r_work: 0.3330 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6072 Z= 0.173 Angle : 0.567 9.390 8837 Z= 0.307 Chirality : 0.040 0.635 1089 Planarity : 0.004 0.035 621 Dihedral : 21.567 166.272 2488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.41 % Allowed : 13.31 % Favored : 83.28 % 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: 0.31 (0.49), residues: 331 helix: 1.22 (0.41), residues: 174 sheet: 0.86 (1.13), residues: 10 loop : -1.09 (0.57), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.002 PHE A 570 TYR 0.012 0.002 TYR A 76 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9050 (mt0) cc_final: 0.8541 (mp10) REVERT: A 579 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8214 (mtpp) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.2311 time to fit residues: 16.0915 Evaluate side-chains 50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103846 restraints weight = 11933.999| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.10 r_work: 0.3379 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6072 Z= 0.124 Angle : 0.522 8.784 8837 Z= 0.285 Chirality : 0.036 0.555 1089 Planarity : 0.004 0.056 621 Dihedral : 21.480 164.523 2488 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.75 % Allowed : 11.60 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.49), residues: 331 helix: 1.54 (0.41), residues: 174 sheet: 0.71 (1.11), residues: 10 loop : -1.05 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 120 HIS 0.001 0.000 HIS A 145 PHE 0.009 0.001 PHE A 236 TYR 0.010 0.002 TYR A 97 ARG 0.004 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8607 (mmm160) REVERT: A 248 GLN cc_start: 0.9054 (mt0) cc_final: 0.8525 (mp10) REVERT: A 579 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8141 (mtpp) REVERT: A 607 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4948 (tt) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 0.2275 time to fit residues: 15.5511 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099972 restraints weight = 11777.155| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.11 r_work: 0.3321 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6072 Z= 0.206 Angle : 0.570 9.262 8837 Z= 0.308 Chirality : 0.039 0.622 1089 Planarity : 0.003 0.033 621 Dihedral : 21.410 164.610 2488 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.41 % Allowed : 11.95 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.49), residues: 331 helix: 1.62 (0.40), residues: 174 sheet: 0.78 (1.07), residues: 10 loop : -1.04 (0.57), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 120 HIS 0.003 0.001 HIS A 91 PHE 0.010 0.001 PHE A 570 TYR 0.014 0.002 TYR A 76 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8963 (mmm160) cc_final: 0.8561 (mmm160) REVERT: A 248 GLN cc_start: 0.9051 (mt0) cc_final: 0.8539 (mp10) REVERT: A 579 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8163 (mtpp) REVERT: A 607 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4813 (tt) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.2623 time to fit residues: 17.2197 Evaluate side-chains 53 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.137803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093701 restraints weight = 11663.468| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.14 r_work: 0.3235 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6072 Z= 0.409 Angle : 0.753 10.956 8837 Z= 0.397 Chirality : 0.050 0.867 1089 Planarity : 0.005 0.047 621 Dihedral : 21.602 169.129 2488 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.75 % Allowed : 11.60 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.19 (0.48), residues: 331 helix: 1.29 (0.39), residues: 176 sheet: 1.30 (1.10), residues: 10 loop : -1.48 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 120 HIS 0.005 0.001 HIS A 91 PHE 0.013 0.002 PHE A 570 TYR 0.017 0.003 TYR A 87 ARG 0.005 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9063 (mt0) cc_final: 0.8572 (mp10) REVERT: A 579 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8237 (mtpp) REVERT: A 607 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5401 (tt) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.2772 time to fit residues: 17.4594 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.140653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096485 restraints weight = 11743.430| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.12 r_work: 0.3282 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6072 Z= 0.226 Angle : 0.610 10.010 8837 Z= 0.328 Chirality : 0.043 0.724 1089 Planarity : 0.004 0.034 621 Dihedral : 21.422 164.563 2488 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.07 % Allowed : 13.31 % Favored : 83.62 % 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: 0.49 (0.50), residues: 331 helix: 1.53 (0.40), residues: 176 sheet: 1.23 (1.07), residues: 10 loop : -1.31 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 570 TYR 0.012 0.002 TYR A 76 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8548 (mmm160) REVERT: A 248 GLN cc_start: 0.9043 (mt0) cc_final: 0.8550 (mp10) REVERT: A 579 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8183 (mtpp) REVERT: A 607 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5280 (tt) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.2704 time to fit residues: 17.0620 Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.136772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092396 restraints weight = 11635.241| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.20 r_work: 0.3211 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6072 Z= 0.381 Angle : 0.722 10.499 8837 Z= 0.381 Chirality : 0.047 0.804 1089 Planarity : 0.005 0.032 621 Dihedral : 21.489 166.948 2488 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.39 % Allowed : 13.99 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.33 (0.49), residues: 331 helix: 1.51 (0.40), residues: 175 sheet: 0.71 (1.03), residues: 10 loop : -1.49 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 120 HIS 0.004 0.001 HIS A 91 PHE 0.012 0.002 PHE A 570 TYR 0.019 0.003 TYR A 169 ARG 0.010 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9054 (mt0) cc_final: 0.8564 (mp10) REVERT: A 579 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8202 (mtpp) REVERT: A 607 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.5972 (tt) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.2945 time to fit residues: 16.9634 Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.139249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095326 restraints weight = 11582.174| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.09 r_work: 0.3265 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6072 Z= 0.238 Angle : 0.617 9.925 8837 Z= 0.331 Chirality : 0.042 0.714 1089 Planarity : 0.004 0.037 621 Dihedral : 21.400 165.068 2488 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.39 % Allowed : 13.65 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.50), residues: 331 helix: 1.72 (0.41), residues: 175 sheet: 0.79 (1.03), residues: 10 loop : -1.35 (0.59), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.002 0.001 HIS A 145 PHE 0.010 0.001 PHE A 570 TYR 0.013 0.002 TYR A 70 ARG 0.008 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8993 (mmm160) cc_final: 0.8583 (mmm160) REVERT: A 248 GLN cc_start: 0.9045 (mt0) cc_final: 0.8546 (mp10) REVERT: A 579 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8274 (mtpp) REVERT: A 607 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5932 (tt) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.2685 time to fit residues: 16.0828 Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.142710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099713 restraints weight = 11688.734| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.13 r_work: 0.3343 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6072 Z= 0.141 Angle : 0.563 9.293 8837 Z= 0.305 Chirality : 0.038 0.621 1089 Planarity : 0.004 0.036 621 Dihedral : 21.370 162.913 2488 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.05 % Allowed : 14.33 % Favored : 83.62 % 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: 0.77 (0.50), residues: 331 helix: 1.82 (0.41), residues: 176 sheet: 1.22 (1.10), residues: 10 loop : -1.26 (0.59), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 127 HIS 0.004 0.001 HIS A 136 PHE 0.009 0.001 PHE A 570 TYR 0.014 0.002 TYR A 70 ARG 0.010 0.001 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9039 (mt0) cc_final: 0.8545 (mp10) REVERT: A 579 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8213 (mtpp) REVERT: A 607 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5617 (tt) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.2586 time to fit residues: 16.4994 Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.143374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100443 restraints weight = 11762.563| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.13 r_work: 0.3353 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6072 Z= 0.140 Angle : 0.550 8.934 8837 Z= 0.297 Chirality : 0.037 0.580 1089 Planarity : 0.003 0.034 621 Dihedral : 21.286 161.344 2488 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 14.33 % Favored : 83.62 % 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: 0.85 (0.51), residues: 331 helix: 1.89 (0.41), residues: 176 sheet: 1.04 (1.13), residues: 10 loop : -1.20 (0.59), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 127 HIS 0.003 0.001 HIS A 136 PHE 0.007 0.001 PHE A 570 TYR 0.011 0.002 TYR A 70 ARG 0.008 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.89 seconds wall clock time: 51 minutes 57.19 seconds (3117.19 seconds total)