Starting phenix.real_space_refine on Thu Mar 6 05:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075.map" model { file = "/net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c07_45075/03_2025/9c07_45075_trim.cif" } resolution = 2.73 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= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 28 5.16 5 C 3050 2.51 5 N 708 2.21 5 O 722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4512 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2108 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2108 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "U" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 148 Unusual residues: {'D12': 4, 'EIC': 1, 'HEX': 8, 'OCT': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 148 Unusual residues: {' K': 4, 'D12': 2, 'EIC': 1, 'HEX': 6, 'OCT': 4, 'R16': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Time building chain proxies: 3.48, per 1000 atoms: 0.77 Number of scatterers: 4512 At special positions: 0 Unit cell: (67.635, 85.17, 98.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 28 16.00 O 722 8.00 N 708 7.00 C 3050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 465.9 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.455A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS U 64 " --> pdb=" O PHE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 83 Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 124 through 166 Proline residue: U 136 - end of helix removed outlier: 3.710A pdb=" N ARG U 166 " --> pdb=" O GLN U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.781A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 295 removed outlier: 3.706A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.451A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 124 through 166 Proline residue: A 136 - end of helix removed outlier: 3.689A pdb=" N ARG A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.518A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.798A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 1.41 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: 757 1.33 - 1.45: 1208 1.45 - 1.57: 2577 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4582 Sorted by residual: bond pdb=" N ILE U 219 " pdb=" CA ILE U 219 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.71e+00 bond pdb=" N HIS U 250 " pdb=" CA HIS U 250 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.28e-02 6.10e+03 4.82e+00 bond pdb=" N TRP U 289 " pdb=" CA TRP U 289 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.79e+00 bond pdb=" N TYR U 251 " pdb=" CA TYR U 251 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.44e-02 4.82e+03 4.53e+00 bond pdb=" C1 EIC U 414 " pdb=" O2 EIC U 414 " ideal model delta sigma weight residual 1.250 1.208 0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 4577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 5924 1.61 - 3.21: 122 3.21 - 4.82: 23 4.82 - 6.43: 4 6.43 - 8.03: 3 Bond angle restraints: 6076 Sorted by residual: angle pdb=" CA TYR U 216 " pdb=" CB TYR U 216 " pdb=" CG TYR U 216 " ideal model delta sigma weight residual 113.90 121.00 -7.10 1.80e+00 3.09e-01 1.55e+01 angle pdb=" N TYR U 216 " pdb=" CA TYR U 216 " pdb=" C TYR U 216 " ideal model delta sigma weight residual 113.28 107.13 6.15 1.57e+00 4.06e-01 1.53e+01 angle pdb=" C MET U 215 " pdb=" N TYR U 216 " pdb=" CA TYR U 216 " ideal model delta sigma weight residual 126.45 119.68 6.77 1.77e+00 3.19e-01 1.46e+01 angle pdb=" N GLU A 252 " pdb=" CA GLU A 252 " pdb=" C GLU A 252 " ideal model delta sigma weight residual 110.80 102.77 8.03 2.13e+00 2.20e-01 1.42e+01 angle pdb=" N ASN A 288 " pdb=" CA ASN A 288 " pdb=" C ASN A 288 " ideal model delta sigma weight residual 111.07 107.44 3.63 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 2340 11.96 - 23.91: 216 23.91 - 35.87: 67 35.87 - 47.82: 36 47.82 - 59.78: 21 Dihedral angle restraints: 2680 sinusoidal: 1162 harmonic: 1518 Sorted by residual: dihedral pdb=" CA ASP U 96 " pdb=" C ASP U 96 " pdb=" N PHE U 97 " pdb=" CA PHE U 97 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 476 0.033 - 0.066: 117 0.066 - 0.099: 33 0.099 - 0.132: 13 0.132 - 0.164: 7 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA THR U 110 " pdb=" N THR U 110 " pdb=" C THR U 110 " pdb=" CB THR U 110 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ALA U 249 " pdb=" N ALA U 249 " pdb=" C ALA U 249 " pdb=" CB ALA U 249 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB THR U 110 " pdb=" CA THR U 110 " pdb=" OG1 THR U 110 " pdb=" CG2 THR U 110 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 643 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 68 " 0.274 9.50e-02 1.11e+02 1.23e-01 9.24e+00 pdb=" NE ARG U 68 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG U 68 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG U 68 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG U 68 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR U 110 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.74e+00 pdb=" C THR U 110 " 0.033 2.00e-02 2.50e+03 pdb=" O THR U 110 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE U 111 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 110 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C THR A 110 " 0.026 2.00e-02 2.50e+03 pdb=" O THR A 110 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 111 " -0.009 2.00e-02 2.50e+03 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 1490 2.84 - 3.42: 4985 3.42 - 3.99: 7754 3.99 - 4.57: 11582 4.57 - 5.14: 16725 Nonbonded interactions: 42536 Sorted by model distance: nonbonded pdb=" OE2 GLU U 220 " pdb=" OH TYR U 257 " model vdw 2.267 3.040 nonbonded pdb=" O SER U 109 " pdb=" OG1 THR U 110 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR U 78 " pdb=" OE2 GLU A 79 " model vdw 2.373 3.040 nonbonded pdb=" O ASN A 277 " pdb=" OG SER A 280 " model vdw 2.384 3.040 nonbonded pdb=" NH1 ARG A 19 " pdb=" OD1 ASN A 288 " model vdw 2.392 3.120 ... (remaining 42531 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 295 or resid 408 or resid 410 through 414)) selection = (chain 'U' and (resid 14 through 295 or resid 408 or resid 410 through 414)) } 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: 1.740 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 0.042 4582 Z= 0.271 Angle : 0.583 8.031 6076 Z= 0.353 Chirality : 0.038 0.164 646 Planarity : 0.005 0.123 732 Dihedral : 12.727 59.778 1708 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.23 % Allowed : 3.60 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.39), residues: 516 helix: 4.11 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.19 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 53 HIS 0.002 0.001 HIS U 64 PHE 0.011 0.001 PHE A 232 TYR 0.010 0.001 TYR A 30 ARG 0.002 0.000 ARG U 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: U 59 GLN cc_start: 0.8808 (tp40) cc_final: 0.8494 (tm-30) REVERT: A 162 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8502 (tm130) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 2.8785 time to fit residues: 191.6836 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.084543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.065893 restraints weight = 8657.913| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.40 r_work: 0.2614 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4582 Z= 0.299 Angle : 0.560 5.295 6076 Z= 0.304 Chirality : 0.036 0.159 646 Planarity : 0.004 0.025 732 Dihedral : 12.372 58.661 772 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.13 % Allowed : 8.11 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.38), residues: 516 helix: 4.05 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.40 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 289 HIS 0.003 0.001 HIS U 64 PHE 0.010 0.001 PHE U 20 TYR 0.018 0.002 TYR A 155 ARG 0.003 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.451 Fit side-chains REVERT: U 65 GLN cc_start: 0.8012 (mp10) cc_final: 0.7701 (mp10) REVERT: U 155 TYR cc_start: 0.7988 (t80) cc_final: 0.7575 (m-80) REVERT: U 251 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 155 TYR cc_start: 0.8022 (t80) cc_final: 0.7612 (t80) REVERT: A 162 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8753 (tm-30) outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 1.8629 time to fit residues: 83.0969 Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 90 ASN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.086714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067749 restraints weight = 8671.520| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.40 r_work: 0.2681 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4582 Z= 0.180 Angle : 0.471 5.048 6076 Z= 0.257 Chirality : 0.033 0.136 646 Planarity : 0.003 0.025 732 Dihedral : 10.830 59.043 772 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.68 % Allowed : 9.23 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.76 (0.38), residues: 516 helix: 4.10 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.47 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.013 0.001 TYR A 155 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.490 Fit side-chains REVERT: U 65 GLN cc_start: 0.7875 (mp10) cc_final: 0.7496 (mp10) REVERT: U 155 TYR cc_start: 0.7884 (t80) cc_final: 0.7553 (t80) REVERT: A 155 TYR cc_start: 0.7973 (t80) cc_final: 0.7559 (t80) outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 2.1821 time to fit residues: 98.7258 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.087546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.068752 restraints weight = 8643.580| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.43 r_work: 0.2700 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4582 Z= 0.179 Angle : 0.466 4.858 6076 Z= 0.255 Chirality : 0.033 0.134 646 Planarity : 0.003 0.022 732 Dihedral : 9.832 59.889 772 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.45 % Allowed : 10.36 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.38), residues: 516 helix: 4.12 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.43 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.011 0.001 TYR A 155 ARG 0.002 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.450 Fit side-chains REVERT: U 65 GLN cc_start: 0.7860 (mp10) cc_final: 0.7583 (mp10) REVERT: U 155 TYR cc_start: 0.7908 (t80) cc_final: 0.7535 (t80) REVERT: A 155 TYR cc_start: 0.7957 (t80) cc_final: 0.7547 (t80) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 1.8670 time to fit residues: 77.2062 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.089274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.070398 restraints weight = 8739.879| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.45 r_work: 0.2733 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4582 Z= 0.158 Angle : 0.450 5.148 6076 Z= 0.246 Chirality : 0.032 0.131 646 Planarity : 0.002 0.022 732 Dihedral : 8.961 58.714 772 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.38), residues: 516 helix: 4.17 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.32 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE A 262 TYR 0.009 0.001 TYR A 155 ARG 0.001 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.453 Fit side-chains REVERT: U 65 GLN cc_start: 0.7748 (mp10) cc_final: 0.7455 (mp10) REVERT: U 155 TYR cc_start: 0.7845 (t80) cc_final: 0.7448 (t80) REVERT: A 155 TYR cc_start: 0.7885 (t80) cc_final: 0.7435 (t80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 2.1603 time to fit residues: 91.0357 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.089337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.070380 restraints weight = 8567.961| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.43 r_work: 0.2732 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4582 Z= 0.163 Angle : 0.458 5.506 6076 Z= 0.249 Chirality : 0.032 0.131 646 Planarity : 0.003 0.031 732 Dihedral : 8.491 57.860 772 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.23 % Allowed : 11.94 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.90 (0.38), residues: 516 helix: 4.17 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.27 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS U 161 PHE 0.007 0.001 PHE A 262 TYR 0.008 0.001 TYR A 155 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.519 Fit side-chains REVERT: U 65 GLN cc_start: 0.7714 (mp10) cc_final: 0.7411 (mp10) REVERT: U 155 TYR cc_start: 0.7856 (t80) cc_final: 0.7451 (t80) REVERT: A 155 TYR cc_start: 0.7762 (t80) cc_final: 0.7319 (t80) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 1.8343 time to fit residues: 77.7243 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.090145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071465 restraints weight = 8536.582| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.42 r_work: 0.2750 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4582 Z= 0.159 Angle : 0.474 7.786 6076 Z= 0.255 Chirality : 0.032 0.130 646 Planarity : 0.002 0.020 732 Dihedral : 7.931 56.552 772 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.45 % Allowed : 12.84 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.38), residues: 516 helix: 4.19 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.20 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.003 0.000 HIS U 161 PHE 0.007 0.001 PHE A 262 TYR 0.007 0.001 TYR A 155 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.509 Fit side-chains REVERT: U 65 GLN cc_start: 0.7708 (mp10) cc_final: 0.7412 (mp10) REVERT: U 155 TYR cc_start: 0.7862 (t80) cc_final: 0.7431 (t80) REVERT: A 48 GLN cc_start: 0.7939 (tt0) cc_final: 0.7685 (mm-40) REVERT: A 110 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7039 (t) REVERT: A 155 TYR cc_start: 0.7765 (t80) cc_final: 0.7301 (t80) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 2.2100 time to fit residues: 96.0696 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.089555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.070775 restraints weight = 8547.107| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.42 r_work: 0.2735 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4582 Z= 0.177 Angle : 0.482 7.359 6076 Z= 0.260 Chirality : 0.032 0.131 646 Planarity : 0.002 0.019 732 Dihedral : 7.763 55.669 772 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.45 % Allowed : 13.29 % Favored : 86.26 % 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: 5.00 (0.38), residues: 516 helix: 4.23 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.19 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.002 0.001 HIS U 161 PHE 0.007 0.001 PHE A 262 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.483 Fit side-chains REVERT: U 65 GLN cc_start: 0.7713 (mp10) cc_final: 0.7419 (mp10) REVERT: A 48 GLN cc_start: 0.7954 (tt0) cc_final: 0.7709 (mm-40) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 2.3099 time to fit residues: 97.4346 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.089292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.070707 restraints weight = 8633.541| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.44 r_work: 0.2724 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4582 Z= 0.182 Angle : 0.491 7.162 6076 Z= 0.265 Chirality : 0.033 0.153 646 Planarity : 0.002 0.019 732 Dihedral : 7.658 54.896 772 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.23 % Allowed : 13.74 % Favored : 86.04 % 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: 5.03 (0.38), residues: 516 helix: 4.19 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.99 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 262 TYR 0.007 0.001 TYR A 30 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.418 Fit side-chains REVERT: U 65 GLN cc_start: 0.7723 (mp10) cc_final: 0.7452 (mp10) REVERT: A 48 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7715 (mm-40) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 2.1023 time to fit residues: 82.6543 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.089124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070239 restraints weight = 8490.260| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.42 r_work: 0.2747 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4582 Z= 0.183 Angle : 0.498 7.578 6076 Z= 0.268 Chirality : 0.033 0.135 646 Planarity : 0.002 0.020 732 Dihedral : 7.525 54.314 772 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % 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: 5.05 (0.38), residues: 516 helix: 4.20 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.97 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE A 262 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.468 Fit side-chains REVERT: U 65 GLN cc_start: 0.7697 (mp10) cc_final: 0.7444 (mp10) REVERT: A 48 GLN cc_start: 0.7928 (tt0) cc_final: 0.7683 (mm-40) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.8465 time to fit residues: 72.4656 Evaluate side-chains 37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.086709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.068090 restraints weight = 8566.627| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.41 r_work: 0.2697 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4582 Z= 0.219 Angle : 0.519 8.015 6076 Z= 0.282 Chirality : 0.034 0.136 646 Planarity : 0.002 0.019 732 Dihedral : 8.123 55.250 772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.23 % Allowed : 13.51 % Favored : 86.26 % 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: 5.00 (0.38), residues: 516 helix: 4.17 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -1.00 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.008 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.52 seconds wall clock time: 72 minutes 21.34 seconds (4341.34 seconds total)