Starting phenix.real_space_refine on Tue Feb 11 11:56:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2s_43757/02_2025/8w2s_43757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2s_43757/02_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_43757/02_2025/8w2s_43757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2s_43757/02_2025/8w2s_43757.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2s_43757/02_2025/8w2s_43757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2s_43757/02_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-5592/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: 4.52, per 1000 atoms: 0.79 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: 1.35 Conformation dependent library (CDL) restraints added in 548.8 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: 2.42 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: 2.29 Time building geometry restraints manager: 1.57 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.340 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- 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 : 0.457 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: 0.2427 time to fit residues: 15.6422 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 : 0.533 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101985 restraints weight = 11805.804| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.12 r_work: 0.3344 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- 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 : 0.460 Fit side-chains REVERT: A 248 GLN cc_start: 0.9064 (mt0) cc_final: 0.8579 (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: 0.2466 time to fit residues: 16.2014 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 : 0.439 ------------------------------------------------------------------------------- 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: 0.3980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.0000 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 133 ASN A 645 ASN A 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102394 restraints weight = 11659.704| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.06 r_work: 0.3354 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6072 Z= 0.154 Angle : 0.556 9.333 8837 Z= 0.302 Chirality : 0.039 0.626 1089 Planarity : 0.004 0.049 621 Dihedral : 21.597 166.342 2488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.07 % Allowed : 13.65 % 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: 0.32 (0.49), residues: 331 helix: 1.23 (0.41), residues: 174 sheet: 0.78 (1.12), residues: 10 loop : -1.08 (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 0.008 0.001 PHE A 570 TYR 0.012 0.002 TYR A 97 ARG 0.003 0.000 ARG A 137 *********************** 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 61 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8718 (mmm160) cc_final: 0.8420 (mmm160) REVERT: A 248 GLN cc_start: 0.9062 (mt0) cc_final: 0.8562 (mp10) REVERT: A 579 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8201 (mtpp) outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.2569 time to fit residues: 17.9196 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.149547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106027 restraints weight = 12055.440| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.08 r_work: 0.3425 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6072 Z= 0.137 Angle : 0.537 9.109 8837 Z= 0.292 Chirality : 0.037 0.594 1089 Planarity : 0.003 0.032 621 Dihedral : 21.523 165.563 2488 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 0.51 (0.49), residues: 331 helix: 1.47 (0.41), residues: 174 sheet: 0.73 (1.08), residues: 10 loop : -1.12 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 PHE 0.013 0.001 PHE A 236 TYR 0.011 0.002 TYR A 97 ARG 0.003 0.000 ARG A 152 *********************** 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 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8712 (t80) cc_final: 0.8474 (t80) REVERT: A 228 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8367 (mmm160) REVERT: A 248 GLN cc_start: 0.9044 (mt0) cc_final: 0.8557 (mp10) REVERT: A 579 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8192 (mtpp) REVERT: A 607 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5171 (tt) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.2532 time to fit residues: 16.2546 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.6980 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: 0.7980 chunk 29 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.148752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105614 restraints weight = 11827.335| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.06 r_work: 0.3421 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6072 Z= 0.142 Angle : 0.530 8.836 8837 Z= 0.288 Chirality : 0.037 0.568 1089 Planarity : 0.003 0.033 621 Dihedral : 21.417 163.978 2488 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.41 % Allowed : 12.63 % 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: 0.73 (0.49), residues: 331 helix: 1.71 (0.41), residues: 174 sheet: 0.71 (1.05), residues: 10 loop : -1.07 (0.57), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 236 TYR 0.012 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 61 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8576 (mmm160) REVERT: A 248 GLN cc_start: 0.9008 (mt0) cc_final: 0.8514 (mp10) REVERT: A 579 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8097 (mtpp) REVERT: A 607 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4839 (tt) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.2325 time to fit residues: 16.8654 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 : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 553 LEU 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: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.140457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095801 restraints weight = 11634.340| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3263 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6072 Z= 0.330 Angle : 0.679 10.391 8837 Z= 0.361 Chirality : 0.046 0.771 1089 Planarity : 0.004 0.038 621 Dihedral : 21.523 167.169 2488 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.10 % Allowed : 12.29 % 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: 0.51 (0.48), residues: 331 helix: 1.53 (0.40), residues: 174 sheet: 1.12 (1.07), residues: 10 loop : -1.22 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 120 HIS 0.005 0.001 HIS A 91 PHE 0.012 0.002 PHE A 570 TYR 0.016 0.003 TYR A 87 ARG 0.003 0.001 ARG A 51 *********************** 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 60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 228 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8683 (mmm160) REVERT: A 248 GLN cc_start: 0.9054 (mt0) cc_final: 0.8548 (mp10) REVERT: A 579 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8206 (mtpp) REVERT: A 607 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5267 (tt) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.3180 time to fit residues: 20.3745 Evaluate side-chains 54 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097488 restraints weight = 11751.025| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.12 r_work: 0.3302 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6072 Z= 0.227 Angle : 0.591 9.710 8837 Z= 0.317 Chirality : 0.042 0.686 1089 Planarity : 0.004 0.032 621 Dihedral : 21.388 165.292 2488 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.73 % Allowed : 12.97 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.50), residues: 331 helix: 1.70 (0.40), residues: 176 sheet: 1.28 (1.11), residues: 10 loop : -1.26 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE A 570 TYR 0.013 0.002 TYR A 76 ARG 0.003 0.001 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 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9037 (mt0) cc_final: 0.8500 (mp10) REVERT: A 579 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8169 (mtpp) REVERT: A 607 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5243 (tt) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.2610 time to fit residues: 16.6214 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 : 0.409 ------------------------------------------------------------------------------- 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: 0.7980 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.139553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095156 restraints weight = 11660.290| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.22 r_work: 0.3255 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6072 Z= 0.304 Angle : 0.648 10.028 8837 Z= 0.345 Chirality : 0.044 0.729 1089 Planarity : 0.004 0.032 621 Dihedral : 21.378 166.037 2488 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.07 % Allowed : 15.02 % Favored : 81.91 % 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: 1.70 (0.40), residues: 176 sheet: 1.36 (1.15), residues: 10 loop : -1.38 (0.57), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 120 HIS 0.003 0.001 HIS A 91 PHE 0.011 0.002 PHE A 570 TYR 0.015 0.002 TYR A 169 ARG 0.004 0.001 ARG A 228 *********************** 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 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7885 (p90) REVERT: A 248 GLN cc_start: 0.9041 (mt0) cc_final: 0.8513 (mp10) REVERT: A 579 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8191 (mtpp) REVERT: A 607 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5502 (tt) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.2504 time to fit residues: 15.3699 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 : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 TYR 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: 0.8980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.098477 restraints weight = 11689.180| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.06 r_work: 0.3310 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6072 Z= 0.194 Angle : 0.584 9.542 8837 Z= 0.314 Chirality : 0.040 0.655 1089 Planarity : 0.003 0.032 621 Dihedral : 21.337 164.522 2488 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.73 % Allowed : 15.36 % Favored : 81.91 % 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: 0.79 (0.50), residues: 331 helix: 1.86 (0.41), residues: 176 sheet: 1.25 (1.13), residues: 10 loop : -1.30 (0.59), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.011 0.001 ARG A 228 *********************** 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 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9037 (mt0) cc_final: 0.8506 (mp10) REVERT: A 579 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8253 (mtpp) REVERT: A 607 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5413 (tt) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.2882 time to fit residues: 18.5851 Evaluate side-chains 50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 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 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 = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099721 restraints weight = 11770.430| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.11 r_work: 0.3331 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6072 Z= 0.166 Angle : 0.574 9.248 8837 Z= 0.308 Chirality : 0.038 0.617 1089 Planarity : 0.004 0.043 621 Dihedral : 21.276 163.132 2488 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.05 % Allowed : 15.36 % Favored : 82.59 % 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: 0.84 (0.50), residues: 331 helix: 1.93 (0.41), residues: 176 sheet: 1.01 (1.08), residues: 10 loop : -1.27 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 127 HIS 0.002 0.001 HIS A 145 PHE 0.009 0.001 PHE A 570 TYR 0.010 0.002 TYR A 76 ARG 0.011 0.001 ARG A 228 ********************** 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 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.8721 (t80) cc_final: 0.8501 (t80) REVERT: A 248 GLN cc_start: 0.9025 (mt0) cc_final: 0.8503 (mp10) REVERT: A 579 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8197 (mtpp) REVERT: A 607 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5433 (tt) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.2751 time to fit residues: 15.7977 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 : 0.484 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099810 restraints weight = 11794.153| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.09 r_work: 0.3333 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 6072 Z= 0.209 Angle : 1.011 59.178 8837 Z= 0.612 Chirality : 0.041 0.616 1089 Planarity : 0.005 0.051 621 Dihedral : 21.289 163.128 2488 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 16.04 % Favored : 82.25 % 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: 0.78 (0.50), residues: 331 helix: 1.87 (0.41), residues: 176 sheet: 0.96 (1.07), residues: 10 loop : -1.28 (0.58), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 120 HIS 0.002 0.000 HIS A 267 PHE 0.009 0.001 PHE A 570 TYR 0.010 0.002 TYR A 76 ARG 0.012 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.62 seconds wall clock time: 52 minutes 30.19 seconds (3150.19 seconds total)