Starting phenix.real_space_refine on Sat May 10 04:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c07_45075/05_2025/9c07_45075_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c07_45075/05_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_45075/05_2025/9c07_45075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c07_45075/05_2025/9c07_45075.map" model { file = "/net/cci-nas-00/data/ceres_data/9c07_45075/05_2025/9c07_45075_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c07_45075/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.47, 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: 1.33 Conformation dependent library (CDL) restraints added in 482.1 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: 0.37 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: 1.28 Time building geometry restraints manager: 1.43 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- 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= 0.227 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 Details of bonding type rmsd hydrogen bonds : bond 0.10002 ( 335) hydrogen bonds : angle 3.54219 ( 1005) covalent geometry : bond 0.00415 ( 4582) covalent geometry : angle 0.58309 ( 6076) *********************** 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 : 0.512 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: 2.0319 time to fit residues: 135.2920 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 : 0.479 ------------------------------------------------------------------------------- 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 = 0.065894 restraints weight = 8657.908| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.40 r_work: 0.2614 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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= 0.194 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 Details of bonding type rmsd hydrogen bonds : bond 0.06541 ( 335) hydrogen bonds : angle 3.13988 ( 1005) covalent geometry : bond 0.00463 ( 4582) covalent geometry : angle 0.56034 ( 6076) *********************** 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 : 0.491 Fit side-chains REVERT: U 65 GLN cc_start: 0.8026 (mp10) cc_final: 0.7716 (mp10) REVERT: U 155 TYR cc_start: 0.7996 (t80) cc_final: 0.7582 (m-80) REVERT: U 251 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6608 (t80) REVERT: A 155 TYR cc_start: 0.8032 (t80) cc_final: 0.7622 (t80) REVERT: A 162 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8762 (tm-30) outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 1.5750 time to fit residues: 70.0755 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 : 0.458 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.087234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.068435 restraints weight = 8684.415| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.43 r_work: 0.2691 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4582 Z= 0.132 Angle : 0.472 5.061 6076 Z= 0.258 Chirality : 0.033 0.136 646 Planarity : 0.003 0.024 732 Dihedral : 10.889 59.097 772 Min Nonbonded Distance : 2.489 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: 4.75 (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 0.006 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 U 292 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 335) hydrogen bonds : angle 2.88806 ( 1005) covalent geometry : bond 0.00284 ( 4582) covalent geometry : angle 0.47212 ( 6076) *********************** 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 : 0.477 Fit side-chains REVERT: U 65 GLN cc_start: 0.7874 (mp10) cc_final: 0.7497 (mp10) REVERT: U 155 TYR cc_start: 0.7886 (t80) cc_final: 0.7551 (t80) REVERT: A 155 TYR cc_start: 0.7972 (t80) cc_final: 0.7557 (t80) outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 1.6539 time to fit residues: 75.0464 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 : 0.447 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070210 restraints weight = 8593.692| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.42 r_work: 0.2716 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4582 Z= 0.116 Angle : 0.453 4.882 6076 Z= 0.248 Chirality : 0.033 0.131 646 Planarity : 0.003 0.022 732 Dihedral : 9.527 59.874 772 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.45 % Allowed : 10.14 % Favored : 89.41 % 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: 4.81 (0.38), residues: 516 helix: 4.13 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.38 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.001 0.000 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.012 0.001 TYR A 155 ARG 0.002 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 335) hydrogen bonds : angle 2.75302 ( 1005) covalent geometry : bond 0.00244 ( 4582) covalent geometry : angle 0.45316 ( 6076) *********************** 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 : 0.561 Fit side-chains REVERT: U 65 GLN cc_start: 0.7760 (mp10) cc_final: 0.7492 (mp10) REVERT: U 155 TYR cc_start: 0.7820 (t80) cc_final: 0.7442 (t80) REVERT: A 155 TYR cc_start: 0.7875 (t80) cc_final: 0.7443 (t80) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 1.6510 time to fit residues: 68.2865 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.087414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.068320 restraints weight = 8761.308| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.42 r_work: 0.2696 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4582 Z= 0.127 Angle : 0.461 4.926 6076 Z= 0.253 Chirality : 0.033 0.134 646 Planarity : 0.002 0.020 732 Dihedral : 9.149 59.191 772 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % 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: 4.85 (0.38), residues: 516 helix: 4.15 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.34 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 262 TYR 0.009 0.001 TYR A 155 ARG 0.001 0.000 ARG U 292 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 335) hydrogen bonds : angle 2.78439 ( 1005) covalent geometry : bond 0.00279 ( 4582) covalent geometry : angle 0.46093 ( 6076) *********************** 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 : 0.448 Fit side-chains REVERT: U 65 GLN cc_start: 0.7779 (mp10) cc_final: 0.7476 (mp10) REVERT: U 155 TYR cc_start: 0.7840 (t80) cc_final: 0.7451 (t80) REVERT: A 155 TYR cc_start: 0.7881 (t80) cc_final: 0.7439 (t80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 1.6464 time to fit residues: 69.6709 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.088023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.068951 restraints weight = 8566.947| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.40 r_work: 0.2718 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4582 Z= 0.122 Angle : 0.462 5.257 6076 Z= 0.252 Chirality : 0.033 0.132 646 Planarity : 0.003 0.029 732 Dihedral : 8.710 58.131 772 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: 4.88 (0.38), residues: 516 helix: 4.16 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.28 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.002 0.001 HIS A 64 PHE 0.007 0.001 PHE A 262 TYR 0.008 0.001 TYR A 155 ARG 0.008 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 335) hydrogen bonds : angle 2.74265 ( 1005) covalent geometry : bond 0.00265 ( 4582) covalent geometry : angle 0.46197 ( 6076) *********************** 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 : 0.474 Fit side-chains REVERT: U 65 GLN cc_start: 0.7758 (mp10) cc_final: 0.7445 (mp10) REVERT: U 155 TYR cc_start: 0.7872 (t80) cc_final: 0.7473 (t80) REVERT: A 155 TYR cc_start: 0.7863 (t80) cc_final: 0.7413 (t80) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 1.6094 time to fit residues: 68.1718 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 : 0.444 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.088364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.069522 restraints weight = 8564.268| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.43 r_work: 0.2715 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4582 Z= 0.125 Angle : 0.487 7.762 6076 Z= 0.263 Chirality : 0.033 0.133 646 Planarity : 0.002 0.020 732 Dihedral : 8.359 57.346 772 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.45 % Allowed : 12.39 % Favored : 87.16 % 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: 4.89 (0.38), residues: 516 helix: 4.15 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.23 (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 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 335) hydrogen bonds : angle 2.74738 ( 1005) covalent geometry : bond 0.00275 ( 4582) covalent geometry : angle 0.48691 ( 6076) *********************** 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 : 0.463 Fit side-chains REVERT: U 65 GLN cc_start: 0.7775 (mp10) cc_final: 0.7466 (mp10) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.6230 time to fit residues: 70.3581 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 10 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.088982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.070104 restraints weight = 8555.425| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.42 r_work: 0.2737 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.003 0.039 4582 Z= 0.121 Angle : 0.489 7.260 6076 Z= 0.264 Chirality : 0.032 0.131 646 Planarity : 0.002 0.020 732 Dihedral : 7.900 56.193 772 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 13.29 % 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: 4.95 (0.38), residues: 516 helix: 4.20 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.22 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE U 232 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 335) hydrogen bonds : angle 2.68886 ( 1005) covalent geometry : bond 0.00263 ( 4582) covalent geometry : angle 0.48912 ( 6076) *********************** 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 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.467 Fit side-chains REVERT: U 65 GLN cc_start: 0.7758 (mp10) cc_final: 0.7463 (mp10) REVERT: U 155 TYR cc_start: 0.7660 (t80) cc_final: 0.7402 (t80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.6307 time to fit residues: 67.3216 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 : 0.474 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.087461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068516 restraints weight = 8603.613| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.44 r_work: 0.2697 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4582 Z= 0.137 Angle : 0.510 7.120 6076 Z= 0.277 Chirality : 0.033 0.135 646 Planarity : 0.002 0.019 732 Dihedral : 8.185 56.181 772 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: 4.95 (0.38), residues: 516 helix: 4.20 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -1.23 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE U 232 TYR 0.008 0.001 TYR A 30 ARG 0.002 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.05252 ( 335) hydrogen bonds : angle 2.78415 ( 1005) covalent geometry : bond 0.00310 ( 4582) covalent geometry : angle 0.51023 ( 6076) *********************** 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 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.524 Fit side-chains REVERT: U 65 GLN cc_start: 0.7782 (mp10) cc_final: 0.7484 (mp10) REVERT: U 155 TYR cc_start: 0.7662 (t80) cc_final: 0.7412 (t80) REVERT: A 155 TYR cc_start: 0.7537 (t80) cc_final: 0.7319 (t80) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.5997 time to fit residues: 66.2882 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 : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.089740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.070617 restraints weight = 8460.947| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.43 r_work: 0.2751 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4582 Z= 0.119 Angle : 0.497 7.446 6076 Z= 0.268 Chirality : 0.033 0.151 646 Planarity : 0.002 0.020 732 Dihedral : 7.656 54.612 772 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % 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: 5.02 (0.38), residues: 516 helix: 4.19 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -1.01 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE U 232 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 335) hydrogen bonds : angle 2.65932 ( 1005) covalent geometry : bond 0.00256 ( 4582) covalent geometry : angle 0.49685 ( 6076) ********************** 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 : 0.413 Fit side-chains REVERT: U 65 GLN cc_start: 0.7660 (mp10) cc_final: 0.7406 (mp10) REVERT: U 155 TYR cc_start: 0.7596 (t80) cc_final: 0.7354 (t80) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 1.6434 time to fit residues: 64.4714 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 : 0.443 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.087927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069110 restraints weight = 8487.914| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.43 r_work: 0.2723 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2062 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= 0.131 Angle : 0.512 8.135 6076 Z= 0.277 Chirality : 0.033 0.138 646 Planarity : 0.002 0.019 732 Dihedral : 7.880 54.814 772 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 13.29 % 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: 5.01 (0.38), residues: 516 helix: 4.18 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -1.01 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 95 HIS 0.003 0.001 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 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 335) hydrogen bonds : angle 2.72352 ( 1005) covalent geometry : bond 0.00293 ( 4582) covalent geometry : angle 0.51169 ( 6076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.30 seconds wall clock time: 53 minutes 25.53 seconds (3205.53 seconds total)