Starting phenix.real_space_refine on Wed Sep 17 05:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gik_51373/09_2025/9gik_51373.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3410 2.51 5 N 918 2.21 5 O 971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5321 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 40, 'TRANS': 598} Chain breaks: 2 Time building chain proxies: 1.70, per 1000 atoms: 0.32 Number of scatterers: 5321 At special positions: 0 Unit cell: (75.8576, 79.192, 117.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 971 8.00 N 918 7.00 C 3410 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: 0.66 Conformation dependent library (CDL) restraints added in 249.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 39.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.745A pdb=" N GLY A 39 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.867A pdb=" N ASP A 258 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.708A pdb=" N LEU A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.632A pdb=" N ILE A 607 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.642A pdb=" N SER A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 704 removed outlier: 3.502A pdb=" N THR A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 721 removed outlier: 3.758A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 removed outlier: 3.818A pdb=" N SER A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 746 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 783 through 796 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.556A pdb=" N GLY A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.907A pdb=" N LEU A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.588A pdb=" N HIS A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 870 Processing helix chain 'A' and resid 871 through 884 Processing helix chain 'A' and resid 892 through 895 removed outlier: 3.597A pdb=" N GLU A 895 " --> pdb=" O GLY A 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 892 through 895' Processing helix chain 'A' and resid 933 through 948 removed outlier: 3.621A pdb=" N MET A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 5.191A pdb=" N VAL A 24 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A 151 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL A 26 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS A 149 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 28 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 62 removed outlier: 6.117A pdb=" N GLU A 57 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 51 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 538 Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 602 removed outlier: 5.816A pdb=" N MET A 600 " --> pdb=" O GLU A 631 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 761 Processing sheet with id=AA8, first strand: chain 'A' and resid 847 through 850 removed outlier: 3.753A pdb=" N GLN A 909 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 897 through 898 removed outlier: 4.000A pdb=" N GLY A 901 " --> pdb=" O GLY A 898 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 534 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: 0.89 Time building geometry restraints manager: 0.82 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: 1001 1.33 - 1.45: 1416 1.45 - 1.57: 3009 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5465 Sorted by residual: bond pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta sigma weight residual 1.472 1.435 0.037 1.17e-02 7.31e+03 9.85e+00 bond pdb=" C PRO A 154 " pdb=" O PRO A 154 " ideal model delta sigma weight residual 1.233 1.205 0.027 9.60e-03 1.09e+04 8.17e+00 bond pdb=" N MET A 153 " pdb=" CA MET A 153 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.04e-02 9.25e+03 3.02e+00 bond pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" N TYR A 152 " pdb=" CA TYR A 152 " ideal model delta sigma weight residual 1.460 1.479 -0.019 1.20e-02 6.94e+03 2.54e+00 ... (remaining 5460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 7314 2.01 - 4.01: 65 4.01 - 6.02: 13 6.02 - 8.03: 2 8.03 - 10.03: 1 Bond angle restraints: 7395 Sorted by residual: angle pdb=" N LYS A 155 " pdb=" CA LYS A 155 " pdb=" C LYS A 155 " ideal model delta sigma weight residual 111.28 101.25 10.03 1.09e+00 8.42e-01 8.48e+01 angle pdb=" C PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 111.40 104.65 6.75 9.10e-01 1.21e+00 5.50e+01 angle pdb=" O LYS A 155 " pdb=" C LYS A 155 " pdb=" N ASN A 156 " ideal model delta sigma weight residual 122.12 126.71 -4.59 1.06e+00 8.90e-01 1.87e+01 angle pdb=" CA LYS A 155 " pdb=" C LYS A 155 " pdb=" O LYS A 155 " ideal model delta sigma weight residual 120.55 116.03 4.52 1.06e+00 8.90e-01 1.82e+01 angle pdb=" N PRO A 154 " pdb=" CA PRO A 154 " pdb=" CB PRO A 154 " ideal model delta sigma weight residual 103.23 105.77 -2.54 6.70e-01 2.23e+00 1.43e+01 ... (remaining 7390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.55: 3019 11.55 - 23.09: 188 23.09 - 34.63: 68 34.63 - 46.18: 12 46.18 - 57.72: 3 Dihedral angle restraints: 3290 sinusoidal: 1414 harmonic: 1876 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N PRO A 154 " pdb=" CA PRO A 154 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA HIS A 549 " pdb=" C HIS A 549 " pdb=" N ASN A 550 " pdb=" CA ASN A 550 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS A 155 " pdb=" CB LYS A 155 " pdb=" CG LYS A 155 " pdb=" CD LYS A 155 " ideal model delta sinusoidal sigma weight residual -60.00 -117.72 57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 540 0.037 - 0.073: 175 0.073 - 0.110: 36 0.110 - 0.146: 11 0.146 - 0.183: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA TYR A 152 " pdb=" N TYR A 152 " pdb=" C TYR A 152 " pdb=" CB TYR A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LYS A 155 " pdb=" N LYS A 155 " pdb=" C LYS A 155 " pdb=" CB LYS A 155 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA ILE A 594 " pdb=" N ILE A 594 " pdb=" C ILE A 594 " pdb=" CB ILE A 594 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 761 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 151 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ALA A 151 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA A 151 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 152 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 118 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLU A 118 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 118 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 119 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 657 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO A 658 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 658 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 658 " 0.016 5.00e-02 4.00e+02 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1087 2.78 - 3.31: 4868 3.31 - 3.84: 8156 3.84 - 4.37: 9883 4.37 - 4.90: 16984 Nonbonded interactions: 40978 Sorted by model distance: nonbonded pdb=" OG SER A 666 " pdb=" OG1 THR A 672 " model vdw 2.248 3.040 nonbonded pdb=" NH1 ARG A 252 " pdb=" O CYS A 833 " model vdw 2.310 3.120 nonbonded pdb=" OH TYR A 612 " pdb=" OG SER A 688 " model vdw 2.313 3.040 nonbonded pdb=" OE1 GLN A 242 " pdb=" NZ LYS A 653 " model vdw 2.322 3.120 nonbonded pdb=" NE ARG A 695 " pdb=" OE1 GLU A 813 " model vdw 2.324 3.120 ... (remaining 40973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.260 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.020 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.003 0.038 5465 Z= 0.140 Angle : 0.509 10.035 7395 Z= 0.311 Chirality : 0.039 0.183 764 Planarity : 0.004 0.029 968 Dihedral : 8.970 57.725 2078 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.23 % Allowed : 4.11 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.34), residues: 633 helix: 0.07 (0.35), residues: 197 sheet: -0.51 (0.47), residues: 123 loop : -0.58 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 799 TYR 0.011 0.001 TYR A 152 PHE 0.007 0.001 PHE A 905 TRP 0.006 0.001 TRP A 864 HIS 0.002 0.001 HIS A 686 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5465) covalent geometry : angle 0.50876 ( 7395) hydrogen bonds : bond 0.23781 ( 203) hydrogen bonds : angle 7.96457 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.185 Fit side-chains REVERT: A 46 LYS cc_start: 0.7406 (tttt) cc_final: 0.7121 (mmtp) REVERT: A 237 ILE cc_start: 0.9228 (mt) cc_final: 0.9018 (mm) REVERT: A 708 ASP cc_start: 0.7945 (t0) cc_final: 0.7706 (t0) REVERT: A 849 TYR cc_start: 0.8224 (m-80) cc_final: 0.8002 (m-80) outliers start: 13 outliers final: 4 residues processed: 101 average time/residue: 0.0918 time to fit residues: 11.8132 Evaluate side-chains 68 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 757 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 555 GLN A 579 GLN A 909 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096403 restraints weight = 9493.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097855 restraints weight = 7522.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098657 restraints weight = 5729.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098821 restraints weight = 5313.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099022 restraints weight = 4830.243| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5465 Z= 0.131 Angle : 0.564 9.935 7395 Z= 0.283 Chirality : 0.041 0.136 764 Planarity : 0.004 0.043 968 Dihedral : 4.334 45.637 715 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.23 % Allowed : 9.25 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.34), residues: 633 helix: 0.80 (0.36), residues: 197 sheet: -0.72 (0.48), residues: 120 loop : -0.37 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.009 0.001 TYR A 581 PHE 0.008 0.001 PHE A 128 TRP 0.008 0.001 TRP A 864 HIS 0.003 0.001 HIS A 920 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5465) covalent geometry : angle 0.56432 ( 7395) hydrogen bonds : bond 0.04620 ( 203) hydrogen bonds : angle 5.78002 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.285 Fit side-chains REVERT: A 46 LYS cc_start: 0.7452 (tttt) cc_final: 0.7232 (mmtp) REVERT: A 683 ASN cc_start: 0.7467 (t0) cc_final: 0.7221 (t0) REVERT: A 708 ASP cc_start: 0.7743 (t0) cc_final: 0.7428 (t0) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.0689 time to fit residues: 7.1783 Evaluate side-chains 67 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 757 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 16 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 57 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.095468 restraints weight = 9479.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095958 restraints weight = 6724.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097065 restraints weight = 5666.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097677 restraints weight = 4527.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097990 restraints weight = 4369.742| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5465 Z= 0.122 Angle : 0.526 8.404 7395 Z= 0.263 Chirality : 0.040 0.130 764 Planarity : 0.004 0.030 968 Dihedral : 4.409 46.987 715 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 8.22 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.33), residues: 633 helix: 0.86 (0.36), residues: 199 sheet: -0.83 (0.46), residues: 122 loop : -0.37 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.008 0.001 TYR A 581 PHE 0.008 0.001 PHE A 649 TRP 0.008 0.001 TRP A 864 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5465) covalent geometry : angle 0.52594 ( 7395) hydrogen bonds : bond 0.03638 ( 203) hydrogen bonds : angle 5.35227 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7409 (tttt) cc_final: 0.7102 (mmtp) REVERT: A 708 ASP cc_start: 0.8020 (t0) cc_final: 0.7571 (t0) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.0620 time to fit residues: 6.6188 Evaluate side-chains 69 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.123913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095425 restraints weight = 9444.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.095872 restraints weight = 6570.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097357 restraints weight = 5588.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097724 restraints weight = 4341.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098084 restraints weight = 4247.998| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5465 Z= 0.120 Angle : 0.514 7.150 7395 Z= 0.260 Chirality : 0.040 0.134 764 Planarity : 0.004 0.028 968 Dihedral : 4.437 50.385 713 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.05 % Allowed : 9.59 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.34), residues: 633 helix: 0.93 (0.36), residues: 199 sheet: -1.17 (0.44), residues: 132 loop : -0.40 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 799 TYR 0.010 0.001 TYR A 849 PHE 0.016 0.001 PHE A 128 TRP 0.007 0.001 TRP A 864 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5465) covalent geometry : angle 0.51409 ( 7395) hydrogen bonds : bond 0.03211 ( 203) hydrogen bonds : angle 5.08074 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.199 Fit side-chains REVERT: A 46 LYS cc_start: 0.7389 (tttt) cc_final: 0.7081 (mmtp) REVERT: A 708 ASP cc_start: 0.8043 (t0) cc_final: 0.7637 (t0) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.0690 time to fit residues: 6.6058 Evaluate side-chains 66 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 880 GLN A 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091688 restraints weight = 9672.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092172 restraints weight = 7573.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093157 restraints weight = 6014.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093730 restraints weight = 5316.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093850 restraints weight = 4866.583| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5465 Z= 0.213 Angle : 0.579 7.449 7395 Z= 0.295 Chirality : 0.043 0.137 764 Planarity : 0.004 0.028 968 Dihedral : 4.797 52.757 713 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.74 % Allowed : 10.79 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.33), residues: 633 helix: 0.66 (0.36), residues: 199 sheet: -1.31 (0.45), residues: 121 loop : -0.53 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 877 TYR 0.013 0.001 TYR A 581 PHE 0.020 0.002 PHE A 128 TRP 0.010 0.001 TRP A 864 HIS 0.004 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 5465) covalent geometry : angle 0.57860 ( 7395) hydrogen bonds : bond 0.03625 ( 203) hydrogen bonds : angle 5.14664 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.252 Fit side-chains REVERT: A 46 LYS cc_start: 0.7475 (tttt) cc_final: 0.7238 (mmtp) REVERT: A 708 ASP cc_start: 0.7959 (t0) cc_final: 0.7593 (t0) REVERT: A 757 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 848 ILE cc_start: 0.8991 (mp) cc_final: 0.8790 (mt) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.0635 time to fit residues: 6.2215 Evaluate side-chains 67 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 26 optimal weight: 0.0070 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 overall best weight: 0.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 826 ASN A 880 GLN A 909 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096590 restraints weight = 9576.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097718 restraints weight = 6631.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098932 restraints weight = 4887.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099268 restraints weight = 4298.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099571 restraints weight = 3997.528| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5465 Z= 0.089 Angle : 0.506 8.080 7395 Z= 0.256 Chirality : 0.040 0.151 764 Planarity : 0.004 0.029 968 Dihedral : 4.523 53.796 713 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.71 % Allowed : 11.99 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.34), residues: 633 helix: 1.00 (0.37), residues: 200 sheet: -1.04 (0.45), residues: 122 loop : -0.45 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.005 0.001 TYR A 689 PHE 0.011 0.001 PHE A 131 TRP 0.005 0.001 TRP A 910 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 5465) covalent geometry : angle 0.50649 ( 7395) hydrogen bonds : bond 0.02788 ( 203) hydrogen bonds : angle 4.79916 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7373 (tttt) cc_final: 0.7038 (mmtp) REVERT: A 122 MET cc_start: 0.7717 (ptm) cc_final: 0.7194 (ptp) REVERT: A 708 ASP cc_start: 0.8040 (t0) cc_final: 0.7639 (t0) REVERT: A 757 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (mp) outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.0619 time to fit residues: 5.9646 Evaluate side-chains 61 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 757 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 880 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095057 restraints weight = 9618.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095102 restraints weight = 7289.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095588 restraints weight = 6188.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096079 restraints weight = 5503.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096697 restraints weight = 5089.049| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5465 Z= 0.163 Angle : 0.537 7.874 7395 Z= 0.271 Chirality : 0.041 0.152 764 Planarity : 0.004 0.028 968 Dihedral : 4.568 53.759 713 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 11.99 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.34), residues: 633 helix: 0.90 (0.36), residues: 200 sheet: -1.06 (0.47), residues: 116 loop : -0.43 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 795 TYR 0.010 0.001 TYR A 581 PHE 0.010 0.001 PHE A 577 TRP 0.008 0.001 TRP A 864 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5465) covalent geometry : angle 0.53686 ( 7395) hydrogen bonds : bond 0.03111 ( 203) hydrogen bonds : angle 4.87821 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.200 Fit side-chains REVERT: A 46 LYS cc_start: 0.7418 (tttt) cc_final: 0.7157 (mttm) REVERT: A 708 ASP cc_start: 0.7913 (t0) cc_final: 0.7554 (t0) REVERT: A 757 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8589 (mp) outliers start: 14 outliers final: 11 residues processed: 68 average time/residue: 0.0617 time to fit residues: 6.0163 Evaluate side-chains 67 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 947 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.122587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095659 restraints weight = 9458.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096383 restraints weight = 6843.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096767 restraints weight = 5824.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097147 restraints weight = 5403.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097431 restraints weight = 4906.072| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5465 Z= 0.131 Angle : 0.520 7.675 7395 Z= 0.263 Chirality : 0.040 0.144 764 Planarity : 0.004 0.028 968 Dihedral : 4.633 55.133 713 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.23 % Allowed : 11.82 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.34), residues: 633 helix: 0.91 (0.36), residues: 200 sheet: -1.07 (0.47), residues: 116 loop : -0.45 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 23 TYR 0.008 0.001 TYR A 581 PHE 0.008 0.001 PHE A 905 TRP 0.006 0.001 TRP A 864 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5465) covalent geometry : angle 0.52041 ( 7395) hydrogen bonds : bond 0.02956 ( 203) hydrogen bonds : angle 4.80411 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.141 Fit side-chains REVERT: A 46 LYS cc_start: 0.7395 (tttt) cc_final: 0.7193 (mmtp) REVERT: A 708 ASP cc_start: 0.7869 (t0) cc_final: 0.7513 (t0) REVERT: A 757 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8578 (mp) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.0697 time to fit residues: 6.4678 Evaluate side-chains 64 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 822 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.121486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.094158 restraints weight = 9766.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094360 restraints weight = 7668.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095344 restraints weight = 6136.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095934 restraints weight = 5245.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096108 restraints weight = 4822.524| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5465 Z= 0.137 Angle : 0.527 7.637 7395 Z= 0.266 Chirality : 0.041 0.138 764 Planarity : 0.004 0.033 968 Dihedral : 4.648 55.911 713 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.88 % Allowed : 12.33 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.34), residues: 633 helix: 0.90 (0.36), residues: 200 sheet: -0.99 (0.48), residues: 114 loop : -0.48 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 645 TYR 0.011 0.001 TYR A 849 PHE 0.009 0.001 PHE A 905 TRP 0.007 0.001 TRP A 864 HIS 0.002 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5465) covalent geometry : angle 0.52683 ( 7395) hydrogen bonds : bond 0.02980 ( 203) hydrogen bonds : angle 4.80230 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.226 Fit side-chains REVERT: A 46 LYS cc_start: 0.7405 (tttt) cc_final: 0.7123 (mmtp) REVERT: A 708 ASP cc_start: 0.7969 (t0) cc_final: 0.7576 (t0) REVERT: A 757 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8561 (mp) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0676 time to fit residues: 6.0905 Evaluate side-chains 65 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 822 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 16 optimal weight: 0.0980 chunk 54 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 880 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095514 restraints weight = 9780.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.097626 restraints weight = 6779.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099077 restraints weight = 5330.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100069 restraints weight = 4545.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100598 restraints weight = 4080.441| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5465 Z= 0.089 Angle : 0.513 7.615 7395 Z= 0.258 Chirality : 0.040 0.149 764 Planarity : 0.004 0.030 968 Dihedral : 4.526 55.875 713 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 12.33 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.34), residues: 633 helix: 1.09 (0.37), residues: 200 sheet: -0.90 (0.49), residues: 112 loop : -0.44 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 98 TYR 0.005 0.001 TYR A 849 PHE 0.008 0.001 PHE A 577 TRP 0.006 0.001 TRP A 910 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 5465) covalent geometry : angle 0.51272 ( 7395) hydrogen bonds : bond 0.02630 ( 203) hydrogen bonds : angle 4.65767 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.217 Fit side-chains REVERT: A 46 LYS cc_start: 0.7412 (tttt) cc_final: 0.7107 (mmtp) REVERT: A 708 ASP cc_start: 0.7938 (t0) cc_final: 0.7549 (t0) REVERT: A 757 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8588 (mp) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.0648 time to fit residues: 6.2228 Evaluate side-chains 63 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 822 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN A 880 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093336 restraints weight = 9770.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094061 restraints weight = 7633.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094923 restraints weight = 5604.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095174 restraints weight = 5094.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095429 restraints weight = 4812.689| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5465 Z= 0.171 Angle : 0.563 7.690 7395 Z= 0.285 Chirality : 0.042 0.144 764 Planarity : 0.004 0.031 968 Dihedral : 4.713 56.372 713 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.88 % Allowed : 12.67 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.34), residues: 633 helix: 0.93 (0.37), residues: 200 sheet: -1.03 (0.48), residues: 114 loop : -0.47 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 645 TYR 0.011 0.001 TYR A 581 PHE 0.011 0.001 PHE A 905 TRP 0.009 0.001 TRP A 864 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5465) covalent geometry : angle 0.56341 ( 7395) hydrogen bonds : bond 0.03223 ( 203) hydrogen bonds : angle 4.84452 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1086.41 seconds wall clock time: 19 minutes 29.17 seconds (1169.17 seconds total)